Starting phenix.real_space_refine on Tue Aug 4 18:02:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pdo_17616/08_2026/8pdo_17616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdo_17616/08_2026/8pdo_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_2026/8pdo_17616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdo_17616/08_2026/8pdo_17616.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8pdo_17616/08_2026/8pdo_17616.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pdo_17616/08_2026/8pdo_17616.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pdo_17616/08_2026/8pdo_17616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdo_17616/08_2026/8pdo_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 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: 1.04, per 1000 atoms: 0.18 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: 0.34 Conformation dependent library (CDL) restraints added in 189.0 milliseconds 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: 0.41 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: 0.57 Time building geometry restraints manager: 0.44 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: 7516 1.43 - 2.86: 365 2.86 - 4.29: 46 4.29 - 5.72: 7 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: 3164 17.53 - 35.05: 323 35.05 - 52.58: 66 52.58 - 70.11: 21 70.11 - 87.64: 21 Dihedral angle restraints: 3595 sinusoidal: 1563 harmonic: 2032 Sorted by residual: dihedral pdb=" C4' C C 74 " pdb=" C3' C C 74 " pdb=" C2' C C 74 " pdb=" C1' C C 74 " ideal model delta sinusoidal sigma weight residual 36.35 -33.10 69.45 1 3.10e+00 1.04e-01 6.48e+02 dihedral pdb=" C4' C C 67 " pdb=" C3' C C 67 " pdb=" C2' C C 67 " pdb=" C1' C C 67 " ideal model delta sinusoidal sigma weight residual 36.35 -32.33 68.68 1 3.10e+00 1.04e-01 6.36e+02 dihedral pdb=" O4' C C 74 " pdb=" C4' C C 74 " pdb=" C3' C C 74 " pdb=" C2' C C 74 " ideal model delta sinusoidal sigma weight residual -35.15 20.74 -55.89 1 4.00e+00 6.25e-02 2.64e+02 ... (remaining 3592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 768 0.058 - 0.116: 132 0.116 - 0.173: 16 0.173 - 0.231: 16 0.231 - 0.289: 4 Chirality restraints: 936 Sorted by residual: chirality pdb=" P C C 64 " pdb=" OP1 C C 64 " pdb=" OP2 C C 64 " pdb=" O5' C C 64 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C2' C C 67 " pdb=" C3' C C 67 " pdb=" O2' C C 67 " pdb=" C1' C C 67 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C2' C C 74 " pdb=" C3' C C 74 " pdb=" O2' C C 74 " pdb=" C1' C C 74 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (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: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.590 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 0.697 7.149 7938 Z= 0.395 Chirality : 0.053 0.289 936 Planarity : 0.004 0.051 962 Dihedral : 16.278 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 are 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/Z covalent geometry : bond 0.00650 / 0.28 ( 5835) covalent geometry : angle 0.69694 / 0.40 ( 7938) hydrogen bonds : bond 0.12984 / 8.80 ( 336) hydrogen bonds : angle 5.84367 / 3.99 ( 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 : 0.137 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: 0.0877 time to fit residues: 9.1537 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 : 0.238 ------------------------------------------------------------------------------- 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... ** 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 = 0.3826 r_free = 0.3826 target = 0.163949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.145212 restraints weight = 6573.696| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.38 r_work: 0.3455 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1163 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= 0.140 Angle : 0.579 8.226 7938 Z= 0.278 Chirality : 0.048 0.440 936 Planarity : 0.004 0.046 962 Dihedral : 13.107 105.060 987 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.34 % Allowed : 5.37 % 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 are not related in a simple way. whole: 0.84 (0.32), residues: 694 helix: 1.18 (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 0.005 0.000 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/Z covalent geometry : bond 0.00314 / 0.14 ( 5835) covalent geometry : angle 0.57891 / 0.28 ( 7938) hydrogen bonds : bond 0.04621 / 3.19 ( 336) hydrogen bonds : angle 4.41102 / 3.05 ( 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 80 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.201 Fit side-chains REVERT: A 78 ARG cc_start: 0.7492 (mmm160) cc_final: 0.5552 (tpt-90) REVERT: A 266 ARG cc_start: 0.7837 (tmt170) cc_final: 0.4853 (mtt180) REVERT: A 337 MET cc_start: 0.8583 (tpp) cc_final: 0.8337 (mmp) REVERT: B 196 LYS cc_start: 0.7786 (mttt) cc_final: 0.7570 (ttpp) outliers start: 2 outliers final: 0 residues processed: 78 average time/residue: 0.1135 time to fit residues: 10.6111 Evaluate side-chains 70 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3832 r_free = 0.3832 target = 0.165039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.142878 restraints weight = 6581.620| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.65 r_work: 0.3425 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1214 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= 0.176 Angle : 0.551 6.326 7938 Z= 0.275 Chirality : 0.045 0.261 936 Planarity : 0.004 0.043 962 Dihedral : 13.031 127.929 987 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.17 % Allowed : 8.72 % 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 are not related in a simple way. whole: 0.89 (0.33), residues: 694 helix: 1.19 (0.24), residues: 474 sheet: -1.08 (0.88), residues: 30 loop : -0.49 (0.46), 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/Z covalent geometry : bond 0.00415 / 0.18 ( 5835) covalent geometry : angle 0.55091 / 0.27 ( 7938) hydrogen bonds : bond 0.04715 / 3.25 ( 336) hydrogen bonds : angle 4.32959 / 2.98 ( 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 72 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.204 Fit side-chains REVERT: A 78 ARG cc_start: 0.7422 (mmm160) cc_final: 0.5376 (tpt-90) REVERT: A 266 ARG cc_start: 0.7817 (tmt170) cc_final: 0.5615 (tpt170) REVERT: B 196 LYS cc_start: 0.7775 (mttt) cc_final: 0.7490 (ttpp) outliers start: 1 outliers final: 1 residues processed: 71 average time/residue: 0.1108 time to fit residues: 9.5922 Evaluate side-chains 68 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 15 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 45 optimal weight: 0.0030 chunk 63 optimal weight: 0.5980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3577 r_free = 0.3577 target = 0.148547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.127063 restraints weight = 6747.889| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.55 r_work: 0.3451 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5835 Z= 0.119 Angle : 0.506 6.894 7938 Z= 0.247 Chirality : 0.044 0.283 936 Planarity : 0.004 0.041 962 Dihedral : 12.986 131.970 987 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.01 % Allowed : 8.89 % 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 are not related in a simple way. whole: 1.22 (0.33), residues: 694 helix: 1.41 (0.25), residues: 476 sheet: -0.98 (0.89), residues: 30 loop : -0.27 (0.47), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 208 TYR 0.011 0.001 TYR A 338 PHE 0.010 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/Z covalent geometry : bond 0.00268 / 0.12 ( 5835) covalent geometry : angle 0.50572 / 0.25 ( 7938) hydrogen bonds : bond 0.04025 / 2.79 ( 336) hydrogen bonds : angle 4.09536 / 2.82 ( 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 82 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.206 Fit side-chains REVERT: A 78 ARG cc_start: 0.7405 (mmm160) cc_final: 0.5386 (tpt-90) REVERT: A 266 ARG cc_start: 0.7731 (tmt170) cc_final: 0.4786 (mtt180) REVERT: B 117 HIS cc_start: 0.7256 (t70) cc_final: 0.6705 (t70) REVERT: B 139 LEU cc_start: 0.8247 (tp) cc_final: 0.7849 (tt) REVERT: B 196 LYS cc_start: 0.7655 (mttt) cc_final: 0.7400 (ttpp) outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.0918 time to fit residues: 9.1253 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 : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 188 ASN 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: 0.8980 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3703 r_free = 0.3703 target = 0.154950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132880 restraints weight = 6792.726| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.64 r_work: 0.3353 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5835 Z= 0.193 Angle : 0.570 6.358 7938 Z= 0.281 Chirality : 0.047 0.276 936 Planarity : 0.004 0.039 962 Dihedral : 12.960 133.149 987 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.17 % Allowed : 10.23 % Favored : 88.59 % 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: 0.84 (0.33), residues: 694 helix: 1.14 (0.24), residues: 480 sheet: -1.07 (0.88), residues: 30 loop : -0.53 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 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/Z covalent geometry : bond 0.00462 / 0.19 ( 5835) covalent geometry : angle 0.57041 / 0.28 ( 7938) hydrogen bonds : bond 0.04749 / 3.28 ( 336) hydrogen bonds : angle 4.26639 / 2.93 ( 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 79 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.194 Fit side-chains REVERT: A 78 ARG cc_start: 0.7441 (mmm160) cc_final: 0.5386 (tpt-90) REVERT: A 135 MET cc_start: 0.6895 (ttt) cc_final: 0.6655 (ttt) REVERT: A 266 ARG cc_start: 0.7768 (tmt170) cc_final: 0.5519 (tpt170) REVERT: A 284 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7214 (tm-30) REVERT: B 196 LYS cc_start: 0.7683 (mttt) cc_final: 0.7462 (ttpp) REVERT: B 282 LEU cc_start: 0.8679 (mt) cc_final: 0.8408 (mt) outliers start: 7 outliers final: 5 residues processed: 76 average time/residue: 0.0985 time to fit residues: 9.0727 Evaluate side-chains 75 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 188 ASN Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain B residue 276 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 3 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3714 r_free = 0.3714 target = 0.155777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.133980 restraints weight = 6674.593| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.62 r_work: 0.3392 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5835 Z= 0.159 Angle : 0.537 6.835 7938 Z= 0.264 Chirality : 0.046 0.290 936 Planarity : 0.004 0.040 962 Dihedral : 12.918 132.739 987 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.01 % Allowed : 11.58 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.32), residues: 694 helix: 1.21 (0.24), residues: 480 sheet: -1.08 (0.88), residues: 30 loop : -0.57 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 208 TYR 0.013 0.002 TYR A 59 PHE 0.012 0.001 PHE B 224 TRP 0.006 0.001 TRP B 123 HIS 0.003 0.001 HIS A 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 5835) covalent geometry : angle 0.53741 / 0.26 ( 7938) hydrogen bonds : bond 0.04431 / 3.06 ( 336) hydrogen bonds : angle 4.17877 / 2.87 ( 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 75 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.141 Fit side-chains REVERT: A 78 ARG cc_start: 0.7415 (mmm160) cc_final: 0.5367 (tpt-90) REVERT: A 135 MET cc_start: 0.6952 (ttt) cc_final: 0.6706 (ttt) REVERT: A 266 ARG cc_start: 0.7708 (tmt170) cc_final: 0.4583 (mtt180) REVERT: B 282 LEU cc_start: 0.8663 (mt) cc_final: 0.8390 (mt) outliers start: 6 outliers final: 5 residues processed: 72 average time/residue: 0.1003 time to fit residues: 8.8619 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 : 0.156 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3676 r_free = 0.3676 target = 0.152962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.130881 restraints weight = 6787.438| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.66 r_work: 0.3365 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1421 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= 0.179 Angle : 0.554 6.640 7938 Z= 0.273 Chirality : 0.046 0.288 936 Planarity : 0.004 0.039 962 Dihedral : 12.861 132.826 987 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.17 % Allowed : 12.08 % Favored : 86.74 % 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: 0.81 (0.32), residues: 694 helix: 1.15 (0.24), residues: 480 sheet: -1.13 (0.87), residues: 30 loop : -0.62 (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/Z covalent geometry : bond 0.00424 / 0.18 ( 5835) covalent geometry : angle 0.55374 / 0.27 ( 7938) hydrogen bonds : bond 0.04610 / 3.19 ( 336) hydrogen bonds : angle 4.22245 / 2.90 ( 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 78 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.167 Fit side-chains REVERT: A 78 ARG cc_start: 0.7411 (mmm160) cc_final: 0.5357 (tpt-90) REVERT: A 135 MET cc_start: 0.6925 (ttt) cc_final: 0.6629 (ttt) REVERT: A 266 ARG cc_start: 0.7718 (tmt170) cc_final: 0.4586 (mtt180) REVERT: A 284 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7321 (tm-30) REVERT: B 282 LEU cc_start: 0.8674 (mt) cc_final: 0.8400 (mt) outliers start: 7 outliers final: 5 residues processed: 75 average time/residue: 0.0995 time to fit residues: 9.1744 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 : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 55 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 9 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 0.0570 chunk 63 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3727 r_free = 0.3727 target = 0.156731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.135503 restraints weight = 6588.939| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.61 r_work: 0.3395 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5835 Z= 0.149 Angle : 0.527 6.949 7938 Z= 0.259 Chirality : 0.046 0.293 936 Planarity : 0.004 0.039 962 Dihedral : 12.790 132.465 987 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.84 % Allowed : 12.58 % Favored : 86.58 % 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 are not related in a simple way. whole: 0.95 (0.33), residues: 694 helix: 1.26 (0.24), residues: 480 sheet: -1.04 (0.89), residues: 30 loop : -0.62 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 208 TYR 0.012 0.002 TYR A 59 PHE 0.012 0.001 PHE B 224 TRP 0.006 0.001 TRP B 123 HIS 0.003 0.001 HIS A 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 5835) covalent geometry : angle 0.52712 / 0.26 ( 7938) hydrogen bonds : bond 0.04327 / 3.00 ( 336) hydrogen bonds : angle 4.14744 / 2.85 ( 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 77 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.204 Fit side-chains REVERT: A 78 ARG cc_start: 0.7403 (mmm160) cc_final: 0.5357 (tpt-90) REVERT: A 135 MET cc_start: 0.6965 (ttt) cc_final: 0.6659 (ttt) REVERT: A 266 ARG cc_start: 0.7686 (tmt170) cc_final: 0.4560 (mtt180) REVERT: A 284 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7270 (tm-30) REVERT: B 196 LYS cc_start: 0.7640 (mttt) cc_final: 0.7375 (ttpp) REVERT: B 282 LEU cc_start: 0.8666 (mt) cc_final: 0.8399 (mt) outliers start: 5 outliers final: 5 residues processed: 74 average time/residue: 0.1099 time to fit residues: 9.9596 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 : 0.192 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 28 optimal weight: 0.0470 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3882 r_free = 0.3882 target = 0.169721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.151336 restraints weight = 6655.823| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.34 r_work: 0.3586 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1703 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= 0.118 Angle : 0.499 7.021 7938 Z= 0.245 Chirality : 0.044 0.289 936 Planarity : 0.004 0.039 962 Dihedral : 12.616 131.609 987 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.67 % Allowed : 13.09 % Favored : 86.24 % 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: 1.31 (0.33), residues: 694 helix: 1.54 (0.25), residues: 476 sheet: -1.49 (0.74), residues: 38 loop : -0.27 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 208 TYR 0.011 0.001 TYR A 338 PHE 0.010 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/Z covalent geometry : bond 0.00267 / 0.12 ( 5835) covalent geometry : angle 0.49930 / 0.24 ( 7938) hydrogen bonds : bond 0.03934 / 2.73 ( 336) hydrogen bonds : angle 4.00771 / 2.76 ( 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 75 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.199 Fit side-chains REVERT: A 78 ARG cc_start: 0.7566 (mmm160) cc_final: 0.5684 (tpt-90) REVERT: A 135 MET cc_start: 0.7074 (ttt) cc_final: 0.6796 (ttt) REVERT: A 266 ARG cc_start: 0.7744 (tmt170) cc_final: 0.4908 (mtt180) REVERT: A 284 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7397 (tm-30) REVERT: B 117 HIS cc_start: 0.7300 (t70) cc_final: 0.6739 (t70) outliers start: 4 outliers final: 2 residues processed: 72 average time/residue: 0.1021 time to fit residues: 9.0290 Evaluate side-chains 69 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 341 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 21 optimal weight: 0.2980 chunk 42 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 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: 2.9990 chunk 22 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.167797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.149378 restraints weight = 6662.308| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.31 r_work: 0.3527 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1643 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= 0.148 Angle : 0.523 6.596 7938 Z= 0.258 Chirality : 0.045 0.276 936 Planarity : 0.004 0.040 962 Dihedral : 12.617 132.391 987 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.67 % Allowed : 13.59 % 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 are not related in a simple way. whole: 1.13 (0.33), residues: 694 helix: 1.44 (0.24), residues: 480 sheet: -1.54 (0.75), residues: 38 loop : -0.49 (0.47), residues: 176 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 0.012 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/Z covalent geometry : bond 0.00346 / 0.15 ( 5835) covalent geometry : angle 0.52281 / 0.26 ( 7938) hydrogen bonds : bond 0.04243 / 2.94 ( 336) hydrogen bonds : angle 4.08875 / 2.81 ( 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 75 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.222 Fit side-chains REVERT: A 78 ARG cc_start: 0.7570 (mmm160) cc_final: 0.5787 (tpt-90) REVERT: A 135 MET cc_start: 0.7063 (ttt) cc_final: 0.6802 (ttt) REVERT: A 266 ARG cc_start: 0.7772 (tmt170) cc_final: 0.4867 (mtt180) REVERT: A 284 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7370 (tm-30) REVERT: B 117 HIS cc_start: 0.7205 (t70) cc_final: 0.6723 (t70) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.1085 time to fit residues: 9.6655 Evaluate side-chains 73 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 341 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 0.0980 chunk 42 optimal weight: 0.5980 chunk 13 optimal weight: 0.0470 chunk 30 optimal weight: 0.8980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3936 r_free = 0.3936 target = 0.174251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.155964 restraints weight = 6438.513| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.35 r_work: 0.3584 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1757 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= 0.121 Angle : 0.504 6.992 7938 Z= 0.248 Chirality : 0.045 0.286 936 Planarity : 0.004 0.040 962 Dihedral : 12.579 131.867 987 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.50 % Allowed : 13.93 % Favored : 85.57 % 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: 1.39 (0.33), residues: 694 helix: 1.62 (0.24), residues: 476 sheet: -1.52 (0.74), residues: 38 loop : -0.29 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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/Z covalent geometry : bond 0.00273 / 0.12 ( 5835) covalent geometry : angle 0.50405 / 0.25 ( 7938) hydrogen bonds : bond 0.03978 / 2.76 ( 336) hydrogen bonds : angle 4.01775 / 2.77 ( 987) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1394.18 seconds wall clock time: 24 minutes 36.11 seconds (1476.11 seconds total)