Starting phenix.real_space_refine on Wed Jul 1 21:06:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8e_29846/07_2026/8g8e_29846.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8e_29846/07_2026/8g8e_29846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g8e_29846/07_2026/8g8e_29846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8e_29846/07_2026/8g8e_29846.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8e_29846/07_2026/8g8e_29846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8e_29846/07_2026/8g8e_29846.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 64 5.49 5 S 5 5.16 5 C 1357 2.51 5 N 453 2.21 5 O 585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2464 Number of models: 1 Model: "" Number of chains: 3 Chain: "J" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 661 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "I" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 651 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "X" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1152 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Time building chain proxies: 0.81, per 1000 atoms: 0.33 Number of scatterers: 2464 At special positions: 0 Unit cell: (69.96, 76.32, 115.54, 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 5 16.00 P 64 15.00 O 585 8.00 N 453 7.00 C 1357 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: 0.31 Conformation dependent library (CDL) restraints added in 51.0 milliseconds 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 266 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 81.4% alpha, 0.0% beta 31 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'X' and resid 141 through 161 Processing helix chain 'X' and resid 163 through 176 Processing helix chain 'X' and resid 180 through 189 removed outlier: 3.554A pdb=" N ILE X 184 " --> pdb=" O SER X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 193 through 211 Proline residue: X 202 - end of helix Processing helix chain 'X' and resid 215 through 220 Processing helix chain 'X' and resid 238 through 249 Processing helix chain 'X' and resid 256 through 268 removed outlier: 3.681A pdb=" N HIS X 262 " --> pdb=" O GLN X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 288 removed outlier: 4.059A pdb=" N SER X 288 " --> pdb=" O LYS X 284 " (cutoff:3.500A) 76 hydrogen bonds defined for protein. 228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 0.25 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 471 1.33 - 1.45: 884 1.45 - 1.57: 1149 1.57 - 1.69: 126 1.69 - 1.81: 6 Bond restraints: 2636 Sorted by residual: bond pdb=" C3' DC I 75 " pdb=" C2' DC I 75 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.43e+01 bond pdb=" C3' DC I 95 " pdb=" C2' DC I 95 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DT J -71 " pdb=" C2' DT J -71 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG I 80 " pdb=" C2' DG I 80 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.79e+00 bond pdb=" C1' DT J -89 " pdb=" N1 DT J -89 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.39e+00 ... (remaining 2631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 3727 2.38 - 4.76: 85 4.76 - 7.14: 8 7.14 - 9.53: 1 9.53 - 11.91: 1 Bond angle restraints: 3822 Sorted by residual: angle pdb=" N3 DT J -74 " pdb=" C4 DT J -74 " pdb=" O4 DT J -74 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" O4' DG I 85 " pdb=" C4' DG I 85 " pdb=" C3' DG I 85 " ideal model delta sigma weight residual 106.00 103.42 2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT J -78 " pdb=" C4 DT J -78 " pdb=" O4 DT J -78 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT I 90 " pdb=" C4 DT I 90 " pdb=" O4 DT I 90 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT I 76 " pdb=" C4 DT I 76 " pdb=" O4 DT I 76 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 ... (remaining 3817 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 30.43: 1083 30.43 - 60.84: 356 60.84 - 91.26: 2 91.26 - 121.68: 0 121.68 - 152.10: 2 Dihedral angle restraints: 1443 sinusoidal: 1038 harmonic: 405 Sorted by residual: dihedral pdb=" C4' DA I 74 " pdb=" C3' DA I 74 " pdb=" O3' DA I 74 " pdb=" P DC I 75 " ideal model delta sinusoidal sigma weight residual 220.00 67.90 152.10 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" C4' DG J -93 " pdb=" C3' DG J -93 " pdb=" O3' DG J -93 " pdb=" P DG J -92 " ideal model delta sinusoidal sigma weight residual 220.00 81.85 138.15 1 3.50e+01 8.16e-04 1.37e+01 dihedral pdb=" CA GLU X 238 " pdb=" C GLU X 238 " pdb=" N ASN X 239 " pdb=" CA ASN X 239 " ideal model delta harmonic sigma weight residual -180.00 -164.72 -15.28 0 5.00e+00 4.00e-02 9.34e+00 ... (remaining 1440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 219 0.030 - 0.060: 127 0.060 - 0.091: 52 0.091 - 0.121: 23 0.121 - 0.151: 9 Chirality restraints: 430 Sorted by residual: chirality pdb=" C3' DT I 82 " pdb=" C4' DT I 82 " pdb=" O3' DT I 82 " pdb=" C2' DT I 82 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CG LEU X 190 " pdb=" CB LEU X 190 " pdb=" CD1 LEU X 190 " pdb=" CD2 LEU X 190 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" C3' DT I 86 " pdb=" C4' DT I 86 " pdb=" O3' DT I 86 " pdb=" C2' DT I 86 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 427 not shown) Planarity restraints: 263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS X 254 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO X 255 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO X 255 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO X 255 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC J -80 " -0.019 2.00e-02 2.50e+03 9.43e-03 2.00e+00 pdb=" N1 DC J -80 " 0.019 2.00e-02 2.50e+03 pdb=" C2 DC J -80 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC J -80 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DC J -80 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DC J -80 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC J -80 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC J -80 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC J -80 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP X 277 " -0.011 2.00e-02 2.50e+03 8.31e-03 1.72e+00 pdb=" CG TRP X 277 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP X 277 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP X 277 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP X 277 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP X 277 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP X 277 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 277 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 277 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP X 277 " -0.000 2.00e-02 2.50e+03 ... (remaining 260 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 531 2.80 - 3.33: 2248 3.33 - 3.85: 4846 3.85 - 4.38: 5302 4.38 - 4.90: 7197 Nonbonded interactions: 20124 Sorted by model distance: nonbonded pdb=" O GLN X 155 " pdb=" OG1 THR X 159 " model vdw 2.277 3.040 nonbonded pdb=" OP2 DA J -87 " pdb=" ND2 ASN X 196 " model vdw 2.302 3.120 nonbonded pdb=" NE ARG X 157 " pdb=" OE2 GLU X 188 " model vdw 2.303 3.120 nonbonded pdb=" NH2 ARG X 157 " pdb=" OE1 GLU X 188 " model vdw 2.305 3.120 nonbonded pdb=" O LEU X 248 " pdb=" NE2 GLN X 251 " model vdw 2.308 3.120 ... (remaining 20119 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 3.840 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 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 : 0.007 0.041 2636 Z= 0.583 Angle : 0.882 11.907 3822 Z= 0.739 Chirality : 0.048 0.151 430 Planarity : 0.005 0.041 263 Dihedral : 28.395 152.096 1177 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.79 % Allowed : 18.90 % Favored : 80.31 % 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: 0.35 (0.74), residues: 136 helix: 0.74 (0.51), residues: 110 sheet: None (None), residues: 0 loop : -1.73 (1.21), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 234 TYR 0.000 0.000 TYR X 162 PHE 0.011 0.002 PHE X 187 TRP 0.022 0.003 TRP X 277 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.58 ( 2636) covalent geometry : angle 0.88241 / 0.74 ( 3822) hydrogen bonds : bond 0.06481 / 7.26 ( 150) hydrogen bonds : angle 3.84857 / 5.42 ( 376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 149 PHE cc_start: 0.6097 (t80) cc_final: 0.5745 (t80) REVERT: X 273 VAL cc_start: 0.8597 (t) cc_final: 0.8031 (t) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.0851 time to fit residues: 4.4059 Evaluate side-chains 27 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** X 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.032746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.025240 restraints weight = 28652.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.026326 restraints weight = 14935.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.027036 restraints weight = 9594.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.027546 restraints weight = 6869.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.027834 restraints weight = 5323.252| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2636 Z= 0.180 Angle : 0.700 6.277 3822 Z= 0.437 Chirality : 0.045 0.225 430 Planarity : 0.005 0.039 263 Dihedral : 30.778 152.753 865 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.79 % Allowed : 7.09 % Favored : 92.13 % 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: 0.04 (0.72), residues: 136 helix: 0.49 (0.49), residues: 110 sheet: None (None), residues: 0 loop : -1.67 (1.25), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 242 TYR 0.002 0.001 TYR X 162 PHE 0.034 0.003 PHE X 278 TRP 0.026 0.003 TRP X 277 HIS 0.001 0.000 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.18 ( 2636) covalent geometry : angle 0.70006 / 0.44 ( 3822) hydrogen bonds : bond 0.04881 / 5.59 ( 150) hydrogen bonds : angle 3.92140 / 5.52 ( 376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 147 GLU cc_start: 0.9455 (tt0) cc_final: 0.9223 (mt-10) REVERT: X 181 GLN cc_start: 0.8991 (pp30) cc_final: 0.8593 (pp30) REVERT: X 197 MET cc_start: 0.9551 (mmp) cc_final: 0.9347 (mmm) REVERT: X 278 PHE cc_start: 0.9648 (m-80) cc_final: 0.9106 (m-80) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.0580 time to fit residues: 2.0107 Evaluate side-chains 22 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** X 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.030763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.023487 restraints weight = 29993.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.024507 restraints weight = 15710.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.025200 restraints weight = 10185.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.025682 restraints weight = 7384.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.026016 restraints weight = 5811.933| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2636 Z= 0.201 Angle : 0.694 6.570 3822 Z= 0.428 Chirality : 0.043 0.212 430 Planarity : 0.005 0.031 263 Dihedral : 30.879 153.632 865 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % 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: -0.13 (0.69), residues: 136 helix: 0.35 (0.47), residues: 111 sheet: None (None), residues: 0 loop : -1.65 (1.20), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 232 TYR 0.001 0.000 TYR X 162 PHE 0.025 0.003 PHE X 278 TRP 0.036 0.005 TRP X 277 HIS 0.004 0.003 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.20 ( 2636) covalent geometry : angle 0.69431 / 0.43 ( 3822) hydrogen bonds : bond 0.06267 / 7.07 ( 150) hydrogen bonds : angle 3.97255 / 5.62 ( 376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 147 GLU cc_start: 0.9477 (tt0) cc_final: 0.9250 (mt-10) REVERT: X 181 GLN cc_start: 0.9122 (pp30) cc_final: 0.8761 (pp30) REVERT: X 244 ASN cc_start: 0.9543 (m110) cc_final: 0.9338 (m110) REVERT: X 278 PHE cc_start: 0.9776 (m-80) cc_final: 0.9464 (m-80) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0471 time to fit residues: 1.5364 Evaluate side-chains 22 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 2 optimal weight: 9.9990 chunk 12 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** X 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.029652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.022522 restraints weight = 31831.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.023540 restraints weight = 16788.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.024236 restraints weight = 10799.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.024698 restraints weight = 7738.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.024982 restraints weight = 6038.224| |-----------------------------------------------------------------------------| r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2636 Z= 0.179 Angle : 0.653 6.399 3822 Z= 0.402 Chirality : 0.040 0.212 430 Planarity : 0.004 0.026 263 Dihedral : 31.048 153.165 865 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: -0.06 (0.69), residues: 136 helix: 0.40 (0.48), residues: 111 sheet: None (None), residues: 0 loop : -1.66 (1.16), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 186 TYR 0.001 0.000 TYR X 162 PHE 0.013 0.002 PHE X 278 TRP 0.033 0.005 TRP X 277 HIS 0.003 0.002 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.18 ( 2636) covalent geometry : angle 0.65317 / 0.40 ( 3822) hydrogen bonds : bond 0.05120 / 5.79 ( 150) hydrogen bonds : angle 3.95673 / 5.51 ( 376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 181 GLN cc_start: 0.9034 (pp30) cc_final: 0.8669 (pp30) REVERT: X 197 MET cc_start: 0.9653 (mmp) cc_final: 0.9431 (mmm) REVERT: X 244 ASN cc_start: 0.9563 (m110) cc_final: 0.9348 (m110) REVERT: X 278 PHE cc_start: 0.9634 (m-80) cc_final: 0.9335 (m-80) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0583 time to fit residues: 1.8648 Evaluate side-chains 21 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 16 optimal weight: 0.0370 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.029181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.021811 restraints weight = 30449.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.022871 restraints weight = 16089.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.023574 restraints weight = 10444.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.024075 restraints weight = 7585.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.024424 restraints weight = 5924.490| |-----------------------------------------------------------------------------| r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2636 Z= 0.186 Angle : 0.667 7.234 3822 Z= 0.411 Chirality : 0.042 0.207 430 Planarity : 0.004 0.024 263 Dihedral : 31.159 153.367 865 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % 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: -0.06 (0.70), residues: 136 helix: 0.43 (0.49), residues: 111 sheet: None (None), residues: 0 loop : -1.80 (1.04), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 234 TYR 0.001 0.001 TYR X 162 PHE 0.010 0.002 PHE X 187 TRP 0.034 0.009 TRP X 277 HIS 0.003 0.002 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.19 ( 2636) covalent geometry : angle 0.66700 / 0.41 ( 3822) hydrogen bonds : bond 0.05445 / 6.05 ( 150) hydrogen bonds : angle 4.08180 / 5.76 ( 376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 181 GLN cc_start: 0.9101 (pp30) cc_final: 0.8736 (pp30) REVERT: X 197 MET cc_start: 0.9672 (mmp) cc_final: 0.9440 (mmm) REVERT: X 210 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8956 (pt0) REVERT: X 278 PHE cc_start: 0.9647 (m-80) cc_final: 0.9408 (m-80) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0519 time to fit residues: 1.7308 Evaluate side-chains 21 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** X 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.030270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.022586 restraints weight = 29907.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.023649 restraints weight = 15488.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.024372 restraints weight = 9951.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.024846 restraints weight = 7196.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.025099 restraints weight = 5670.472| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2636 Z= 0.153 Angle : 0.647 5.863 3822 Z= 0.399 Chirality : 0.042 0.195 430 Planarity : 0.004 0.028 263 Dihedral : 31.222 153.185 865 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: 0.07 (0.70), residues: 136 helix: 0.57 (0.50), residues: 111 sheet: None (None), residues: 0 loop : -2.04 (0.90), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 234 TYR 0.004 0.001 TYR X 162 PHE 0.011 0.002 PHE X 187 TRP 0.030 0.006 TRP X 207 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.15 ( 2636) covalent geometry : angle 0.64746 / 0.40 ( 3822) hydrogen bonds : bond 0.04353 / 4.77 ( 150) hydrogen bonds : angle 3.84872 / 5.43 ( 376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.066 Fit side-chains revert: symmetry clash REVERT: X 166 ASP cc_start: 0.9720 (m-30) cc_final: 0.9484 (t0) REVERT: X 278 PHE cc_start: 0.9708 (m-80) cc_final: 0.9352 (m-80) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0553 time to fit residues: 1.7762 Evaluate side-chains 20 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.028404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.021119 restraints weight = 30126.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.022147 restraints weight = 15016.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.022830 restraints weight = 9490.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.023286 restraints weight = 6795.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.023570 restraints weight = 5323.984| |-----------------------------------------------------------------------------| r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2636 Z= 0.190 Angle : 0.666 6.199 3822 Z= 0.405 Chirality : 0.041 0.200 430 Planarity : 0.004 0.024 263 Dihedral : 31.263 154.504 865 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.69), residues: 136 helix: 0.41 (0.49), residues: 111 sheet: None (None), residues: 0 loop : -2.19 (0.89), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 234 TYR 0.001 0.000 TYR X 162 PHE 0.010 0.002 PHE X 175 TRP 0.026 0.004 TRP X 277 HIS 0.002 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.19 ( 2636) covalent geometry : angle 0.66634 / 0.41 ( 3822) hydrogen bonds : bond 0.06194 / 6.82 ( 150) hydrogen bonds : angle 4.04004 / 5.53 ( 376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.064 Fit side-chains revert: symmetry clash REVERT: X 166 ASP cc_start: 0.9725 (m-30) cc_final: 0.9457 (t0) REVERT: X 219 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8354 (mt-10) REVERT: X 278 PHE cc_start: 0.9693 (m-80) cc_final: 0.9319 (m-80) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0578 time to fit residues: 1.7713 Evaluate side-chains 19 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** X 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.029145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.021827 restraints weight = 30215.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.022860 restraints weight = 15533.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.023554 restraints weight = 10019.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.024012 restraints weight = 7241.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.024353 restraints weight = 5710.297| |-----------------------------------------------------------------------------| r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2636 Z= 0.169 Angle : 0.674 7.170 3822 Z= 0.410 Chirality : 0.043 0.203 430 Planarity : 0.003 0.019 263 Dihedral : 31.319 153.778 865 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -0.30 (0.68), residues: 136 helix: 0.32 (0.49), residues: 111 sheet: None (None), residues: 0 loop : -2.22 (0.89), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 234 TYR 0.000 0.000 TYR X 162 PHE 0.007 0.002 PHE X 187 TRP 0.047 0.009 TRP X 207 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.17 ( 2636) covalent geometry : angle 0.67366 / 0.41 ( 3822) hydrogen bonds : bond 0.04658 / 5.11 ( 150) hydrogen bonds : angle 4.02051 / 5.44 ( 376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.069 Fit side-chains revert: symmetry clash REVERT: X 166 ASP cc_start: 0.9714 (m-30) cc_final: 0.9487 (t0) REVERT: X 219 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8301 (mt-10) REVERT: X 244 ASN cc_start: 0.9587 (m110) cc_final: 0.9377 (m110) REVERT: X 278 PHE cc_start: 0.9650 (m-10) cc_final: 0.9299 (m-80) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0595 time to fit residues: 1.8401 Evaluate side-chains 19 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 10 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.029594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.021895 restraints weight = 29233.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.022995 restraints weight = 14708.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.023720 restraints weight = 9247.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.024203 restraints weight = 6621.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.024499 restraints weight = 5176.957| |-----------------------------------------------------------------------------| r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2636 Z= 0.156 Angle : 0.668 5.785 3822 Z= 0.410 Chirality : 0.043 0.200 430 Planarity : 0.003 0.023 263 Dihedral : 31.324 154.053 865 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.70), residues: 136 helix: 0.27 (0.50), residues: 111 sheet: None (None), residues: 0 loop : -2.10 (0.90), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 186 TYR 0.001 0.000 TYR X 162 PHE 0.009 0.002 PHE X 187 TRP 0.032 0.005 TRP X 277 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.16 ( 2636) covalent geometry : angle 0.66803 / 0.41 ( 3822) hydrogen bonds : bond 0.04368 / 4.73 ( 150) hydrogen bonds : angle 4.35572 / 5.97 ( 376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.064 Fit side-chains REVERT: X 147 GLU cc_start: 0.9413 (tt0) cc_final: 0.9150 (mt-10) REVERT: X 166 ASP cc_start: 0.9704 (m-30) cc_final: 0.9466 (t0) REVERT: X 196 ASN cc_start: 0.9269 (m-40) cc_final: 0.8853 (m110) REVERT: X 197 MET cc_start: 0.9628 (mmp) cc_final: 0.9427 (mmm) REVERT: X 219 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8325 (mt-10) REVERT: X 278 PHE cc_start: 0.9622 (m-10) cc_final: 0.9347 (m-80) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0471 time to fit residues: 1.5490 Evaluate side-chains 19 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.029156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.021799 restraints weight = 30228.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.022891 restraints weight = 15037.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.023619 restraints weight = 9441.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.024111 restraints weight = 6745.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.024332 restraints weight = 5238.233| |-----------------------------------------------------------------------------| r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 2636 Z= 0.158 Angle : 0.656 6.251 3822 Z= 0.400 Chirality : 0.042 0.197 430 Planarity : 0.003 0.020 263 Dihedral : 31.332 154.580 865 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -0.25 (0.70), residues: 136 helix: 0.37 (0.50), residues: 111 sheet: None (None), residues: 0 loop : -2.23 (0.88), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 232 TYR 0.000 0.000 TYR X 162 PHE 0.007 0.001 PHE X 187 TRP 0.049 0.010 TRP X 207 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.16 ( 2636) covalent geometry : angle 0.65637 / 0.40 ( 3822) hydrogen bonds : bond 0.04411 / 4.77 ( 150) hydrogen bonds : angle 3.95274 / 5.25 ( 376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 272 Ramachandran restraints generated. 136 Oldfield, 0 Emsley, 136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 166 ASP cc_start: 0.9693 (m-30) cc_final: 0.9478 (t0) REVERT: X 196 ASN cc_start: 0.9231 (m-40) cc_final: 0.8815 (m110) REVERT: X 219 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8399 (mt-10) REVERT: X 244 ASN cc_start: 0.9595 (m110) cc_final: 0.9380 (m110) REVERT: X 278 PHE cc_start: 0.9600 (m-10) cc_final: 0.9332 (m-80) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0346 time to fit residues: 1.1609 Evaluate side-chains 20 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.030193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.022522 restraints weight = 30884.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.023599 restraints weight = 15201.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.024293 restraints weight = 9465.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.024743 restraints weight = 6763.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.025063 restraints weight = 5345.091| |-----------------------------------------------------------------------------| r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2636 Z= 0.152 Angle : 0.633 5.629 3822 Z= 0.390 Chirality : 0.042 0.199 430 Planarity : 0.003 0.025 263 Dihedral : 31.345 154.667 865 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -0.59 (0.69), residues: 136 helix: 0.13 (0.49), residues: 112 sheet: None (None), residues: 0 loop : -2.44 (0.91), residues: 24 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 275 TYR 0.001 0.000 TYR X 162 PHE 0.008 0.001 PHE X 187 TRP 0.031 0.005 TRP X 277 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.15 ( 2636) covalent geometry : angle 0.63325 / 0.39 ( 3822) hydrogen bonds : bond 0.04292 / 4.61 ( 150) hydrogen bonds : angle 4.14450 / 5.38 ( 376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 619.67 seconds wall clock time: 11 minutes 18.50 seconds (678.50 seconds total)