Starting phenix.real_space_refine on Tue Aug 4 12:09:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g8e_29846/08_2026/8g8e_29846.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g8e_29846/08_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_29846/08_2026/8g8e_29846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g8e_29846/08_2026/8g8e_29846.map" model { file = "/net/cci-nas-00/data/ceres_data/8g8e_29846/08_2026/8g8e_29846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g8e_29846/08_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-2.2rc3-6140/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: 0.94, per 1000 atoms: 0.38 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: 0.25 Conformation dependent library (CDL) restraints added in 49.7 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: 0.48 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: 0.44 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: 3726 2.38 - 4.76: 86 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: 1.260 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.410 Find NCS groups from input model: 0.010 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:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.460 ------------------------------------------------------------------------------- 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 : 0.888 11.907 3822 Z= 0.744 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 0.88760 / 0.74 ( 3822) hydrogen bonds : bond 0.06481 / 7.27 ( 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 : 0.069 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: 0.8032 (t) outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.0921 time to fit residues: 4.7338 Evaluate side-chains 28 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.063 ------------------------------------------------------------------------------- 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: 2.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.032000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.024145 restraints weight = 29005.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.025213 restraints weight = 15266.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.025919 restraints weight = 9864.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.026394 restraints weight = 7150.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.026737 restraints weight = 5675.967| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2636 Z= 0.187 Angle : 0.716 7.419 3822 Z= 0.439 Chirality : 0.045 0.234 430 Planarity : 0.006 0.040 263 Dihedral : 30.763 152.136 865 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.79 % Allowed : 7.87 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.72), residues: 136 helix: 0.50 (0.49), residues: 110 sheet: None (None), residues: 0 loop : -1.59 (1.26), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 232 TYR 0.003 0.001 TYR X 162 PHE 0.035 0.003 PHE X 278 TRP 0.027 0.004 TRP X 277 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.19 ( 2636) covalent geometry : angle 0.71638 / 0.44 ( 3822) hydrogen bonds : bond 0.05075 / 5.87 ( 150) hydrogen bonds : angle 3.91826 / 5.51 ( 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 30 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.068 Fit side-chains REVERT: X 147 GLU cc_start: 0.9475 (tt0) cc_final: 0.9245 (mt-10) REVERT: X 181 GLN cc_start: 0.8932 (pp30) cc_final: 0.8566 (pp30) REVERT: X 278 PHE cc_start: 0.9738 (m-80) cc_final: 0.9304 (m-80) REVERT: X 280 ASN cc_start: 0.9523 (m110) cc_final: 0.9237 (p0) outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.0704 time to fit residues: 2.5044 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: 0.8980 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 3 optimal weight: 9.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.2869 r_free = 0.2869 target = 0.031856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.023950 restraints weight = 28928.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.025038 restraints weight = 15313.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.025743 restraints weight = 9912.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.026156 restraints weight = 7237.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.026586 restraints weight = 5896.747| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2834 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= 0.161 Angle : 0.678 7.303 3822 Z= 0.420 Chirality : 0.045 0.228 430 Planarity : 0.005 0.036 263 Dihedral : 30.813 152.016 865 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % 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: -0.28 (0.68), residues: 136 helix: 0.22 (0.47), residues: 111 sheet: None (None), residues: 0 loop : -1.59 (1.22), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG X 232 TYR 0.001 0.000 TYR X 162 PHE 0.026 0.002 PHE X 278 TRP 0.031 0.004 TRP X 277 HIS 0.002 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.16 ( 2636) covalent geometry : angle 0.67767 / 0.42 ( 3822) hydrogen bonds : bond 0.04496 / 5.08 ( 150) hydrogen bonds : angle 3.94354 / 5.72 ( 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 28 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.064 Fit side-chains revert: symmetry clash REVERT: X 181 GLN cc_start: 0.9052 (pp30) cc_final: 0.8669 (pp30) REVERT: X 244 ASN cc_start: 0.9530 (m110) cc_final: 0.9309 (m110) REVERT: X 278 PHE cc_start: 0.9729 (m-80) cc_final: 0.9271 (m-80) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0742 time to fit residues: 2.4239 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 : 0.081 ------------------------------------------------------------------------------- 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: 10.0000 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 0.0670 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.030543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.022614 restraints weight = 29869.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.023737 restraints weight = 15380.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.024489 restraints weight = 9809.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.024982 restraints weight = 7064.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.025264 restraints weight = 5535.582| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2636 Z= 0.186 Angle : 0.682 7.026 3822 Z= 0.413 Chirality : 0.042 0.225 430 Planarity : 0.004 0.026 263 Dihedral : 30.988 152.724 865 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % 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: 0.09 (0.69), residues: 136 helix: 0.56 (0.48), residues: 111 sheet: None (None), residues: 0 loop : -1.87 (1.08), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG X 282 TYR 0.001 0.000 TYR X 162 PHE 0.014 0.003 PHE X 278 TRP 0.035 0.005 TRP X 277 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.19 ( 2636) covalent geometry : angle 0.68203 / 0.41 ( 3822) hydrogen bonds : bond 0.05477 / 6.20 ( 150) hydrogen bonds : angle 3.91859 / 5.55 ( 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 28 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 181 GLN cc_start: 0.9040 (pp30) cc_final: 0.8692 (pp30) REVERT: X 278 PHE cc_start: 0.9792 (m-80) cc_final: 0.9517 (m-80) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0601 time to fit residues: 2.0080 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 : 0.045 ------------------------------------------------------------------------------- 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: 4.9990 chunk 4 optimal weight: 9.9990 chunk 16 optimal weight: 0.0170 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6822 ------------------------------------------------------------------------------- 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 = 0.2822 r_free = 0.2822 target = 0.030817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.023140 restraints weight = 29821.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.024205 restraints weight = 15468.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.024916 restraints weight = 9902.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.025379 restraints weight = 7167.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.025737 restraints weight = 5653.472| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2636 Z= 0.152 Angle : 0.647 6.497 3822 Z= 0.397 Chirality : 0.041 0.205 430 Planarity : 0.004 0.045 263 Dihedral : 31.038 152.117 865 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.36 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: 0.07 (0.69), residues: 136 helix: 0.55 (0.49), residues: 111 sheet: None (None), residues: 0 loop : -1.91 (1.02), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG X 275 TYR 0.000 0.000 TYR X 162 PHE 0.012 0.002 PHE X 278 TRP 0.036 0.005 TRP X 277 HIS 0.002 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.15 ( 2636) covalent geometry : angle 0.64660 / 0.40 ( 3822) hydrogen bonds : bond 0.04143 / 4.65 ( 150) hydrogen bonds : angle 3.89744 / 5.51 ( 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 26 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.040 Fit side-chains revert: symmetry clash REVERT: X 181 GLN cc_start: 0.9032 (pp30) cc_final: 0.8661 (pp30) REVERT: X 196 ASN cc_start: 0.9275 (m-40) cc_final: 0.8933 (m110) REVERT: X 197 MET cc_start: 0.9599 (mmp) cc_final: 0.9333 (mmm) REVERT: X 210 GLU cc_start: 0.9411 (mm-30) cc_final: 0.9177 (pt0) REVERT: X 244 ASN cc_start: 0.9570 (m110) cc_final: 0.9366 (m110) REVERT: X 278 PHE cc_start: 0.9710 (m-80) cc_final: 0.9384 (m-80) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0599 time to fit residues: 1.8407 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 : 0.077 ------------------------------------------------------------------------------- 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: 0.8980 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.2827 r_free = 0.2827 target = 0.031126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.023779 restraints weight = 29968.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.024853 restraints weight = 15000.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.025577 restraints weight = 9468.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.026060 restraints weight = 6760.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.026330 restraints weight = 5232.875| |-----------------------------------------------------------------------------| r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3476 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= 0.150 Angle : 0.630 6.378 3822 Z= 0.389 Chirality : 0.040 0.205 430 Planarity : 0.004 0.032 263 Dihedral : 31.028 152.630 865 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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 (0.69), residues: 136 helix: 0.67 (0.49), residues: 111 sheet: None (None), residues: 0 loop : -2.05 (0.97), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 275 TYR 0.001 0.000 TYR X 162 PHE 0.014 0.002 PHE X 278 TRP 0.036 0.005 TRP X 277 HIS 0.002 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.15 ( 2636) covalent geometry : angle 0.63007 / 0.39 ( 3822) hydrogen bonds : bond 0.04293 / 4.80 ( 150) hydrogen bonds : angle 3.75399 / 5.35 ( 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 : 0.064 Fit side-chains revert: symmetry clash REVERT: X 181 GLN cc_start: 0.9040 (pp30) cc_final: 0.8686 (pp30) REVERT: X 196 ASN cc_start: 0.9241 (m-40) cc_final: 0.8879 (m110) REVERT: X 197 MET cc_start: 0.9604 (mmp) cc_final: 0.9335 (mmm) REVERT: X 278 PHE cc_start: 0.9744 (m-80) cc_final: 0.9416 (m-80) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0466 time to fit residues: 1.5254 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 0.0040 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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 = 0.2836 r_free = 0.2836 target = 0.030239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.022428 restraints weight = 28228.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.023553 restraints weight = 14305.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.024318 restraints weight = 9058.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.024841 restraints weight = 6471.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.025210 restraints weight = 5001.907| |-----------------------------------------------------------------------------| r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3816 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= 0.165 Angle : 0.677 6.589 3822 Z= 0.415 Chirality : 0.042 0.204 430 Planarity : 0.004 0.028 263 Dihedral : 31.084 152.798 865 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.54 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: -0.29 (0.69), residues: 136 helix: 0.34 (0.49), residues: 110 sheet: None (None), residues: 0 loop : -2.12 (0.92), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 275 TYR 0.004 0.001 TYR X 162 PHE 0.008 0.001 PHE X 249 TRP 0.040 0.009 TRP X 277 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.16 ( 2636) covalent geometry : angle 0.67718 / 0.41 ( 3822) hydrogen bonds : bond 0.04489 / 4.88 ( 150) hydrogen bonds : angle 4.10165 / 5.82 ( 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 27 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 166 ASP cc_start: 0.9708 (m-30) cc_final: 0.9456 (t0) REVERT: X 181 GLN cc_start: 0.9114 (pp30) cc_final: 0.8725 (pp30) REVERT: X 196 ASN cc_start: 0.9225 (m-40) cc_final: 0.8854 (m110) REVERT: X 197 MET cc_start: 0.9618 (mmp) cc_final: 0.9352 (mmm) REVERT: X 241 VAL cc_start: 0.9636 (t) cc_final: 0.9329 (t) REVERT: X 244 ASN cc_start: 0.9601 (m110) cc_final: 0.9392 (m110) REVERT: X 278 PHE cc_start: 0.9763 (m-10) cc_final: 0.9438 (m-80) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0369 time to fit residues: 1.2566 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.2822 r_free = 0.2822 target = 0.030253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.022265 restraints weight = 29313.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.023457 restraints weight = 14274.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.024258 restraints weight = 8842.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.024784 restraints weight = 6232.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.025159 restraints weight = 4796.952| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2636 Z= 0.160 Angle : 0.671 6.080 3822 Z= 0.413 Chirality : 0.042 0.205 430 Planarity : 0.004 0.026 263 Dihedral : 31.103 152.917 865 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: -0.31 (0.68), residues: 136 helix: 0.32 (0.49), residues: 110 sheet: None (None), residues: 0 loop : -2.10 (0.88), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 275 TYR 0.002 0.001 TYR X 162 PHE 0.009 0.001 PHE X 187 TRP 0.041 0.008 TRP X 277 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.16 ( 2636) covalent geometry : angle 0.67073 / 0.41 ( 3822) hydrogen bonds : bond 0.04292 / 4.64 ( 150) hydrogen bonds : angle 4.07519 / 5.54 ( 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 : 0.048 Fit side-chains revert: symmetry clash REVERT: X 181 GLN cc_start: 0.9176 (pp30) cc_final: 0.8763 (pp30) REVERT: X 196 ASN cc_start: 0.9168 (m-40) cc_final: 0.8818 (m110) REVERT: X 244 ASN cc_start: 0.9547 (m110) cc_final: 0.9303 (m110) REVERT: X 246 GLU cc_start: 0.9379 (mm-30) cc_final: 0.9152 (tp30) REVERT: X 278 PHE cc_start: 0.9650 (m-10) cc_final: 0.9278 (m-80) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0351 time to fit residues: 1.0920 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 : 0.037 ------------------------------------------------------------------------------- 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: 0.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.2822 r_free = 0.2822 target = 0.030325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.022406 restraints weight = 28133.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.023517 restraints weight = 14362.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.024250 restraints weight = 9069.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.024726 restraints weight = 6480.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.025072 restraints weight = 5053.995| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2636 Z= 0.156 Angle : 0.653 5.931 3822 Z= 0.402 Chirality : 0.041 0.205 430 Planarity : 0.004 0.023 263 Dihedral : 31.124 153.193 865 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: -0.41 (0.67), residues: 136 helix: 0.24 (0.48), residues: 110 sheet: None (None), residues: 0 loop : -2.10 (0.87), residues: 26 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 275 TYR 0.006 0.002 TYR X 162 PHE 0.007 0.001 PHE X 187 TRP 0.042 0.005 TRP X 277 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.16 ( 2636) covalent geometry : angle 0.65277 / 0.40 ( 3822) hydrogen bonds : bond 0.04253 / 4.59 ( 150) hydrogen bonds : angle 4.02352 / 5.49 ( 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 24 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.038 Fit side-chains revert: symmetry clash REVERT: X 153 LEU cc_start: 0.9455 (mt) cc_final: 0.9177 (mt) REVERT: X 196 ASN cc_start: 0.9148 (m-40) cc_final: 0.8781 (m110) REVERT: X 197 MET cc_start: 0.9634 (mmp) cc_final: 0.9361 (mmm) REVERT: X 244 ASN cc_start: 0.9613 (m110) cc_final: 0.9403 (m110) REVERT: X 278 PHE cc_start: 0.9787 (m-10) cc_final: 0.9510 (m-80) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0344 time to fit residues: 1.0287 Evaluate side-chains 18 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.037 ------------------------------------------------------------------------------- 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: 0.3980 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.0870 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.2831 r_free = 0.2831 target = 0.031046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.023221 restraints weight = 30374.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.024344 restraints weight = 15307.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.025089 restraints weight = 9650.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.025576 restraints weight = 6926.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.025940 restraints weight = 5431.466| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 2636 Z= 0.153 Angle : 0.672 5.781 3822 Z= 0.409 Chirality : 0.043 0.208 430 Planarity : 0.003 0.021 263 Dihedral : 31.168 153.197 865 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -0.56 (0.67), residues: 136 helix: 0.14 (0.48), residues: 111 sheet: None (None), residues: 0 loop : -2.27 (0.84), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 275 TYR 0.002 0.001 TYR X 162 PHE 0.011 0.001 PHE X 278 TRP 0.041 0.010 TRP X 207 HIS 0.001 0.000 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.15 ( 2636) covalent geometry : angle 0.67235 / 0.41 ( 3822) hydrogen bonds : bond 0.04114 / 4.34 ( 150) hydrogen bonds : angle 3.94392 / 5.39 ( 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 25 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.039 Fit side-chains revert: symmetry clash REVERT: X 196 ASN cc_start: 0.9101 (m-40) cc_final: 0.8747 (m110) REVERT: X 197 MET cc_start: 0.9603 (mmp) cc_final: 0.9364 (mmm) REVERT: X 210 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9152 (pt0) REVERT: X 278 PHE cc_start: 0.9806 (m-10) cc_final: 0.9415 (m-80) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0370 time to fit residues: 1.1371 Evaluate side-chains 16 residues out of total 127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.038 ------------------------------------------------------------------------------- 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: 1.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 0.0370 chunk 6 optimal weight: 0.8980 overall best weight: 0.9460 ------------------------------------------------------------------------------- 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 = 0.2817 r_free = 0.2817 target = 0.030822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.023311 restraints weight = 30313.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.024381 restraints weight = 15146.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.025096 restraints weight = 9520.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.025568 restraints weight = 6844.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.025904 restraints weight = 5350.593| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2636 Z= 0.158 Angle : 0.650 5.772 3822 Z= 0.397 Chirality : 0.041 0.202 430 Planarity : 0.003 0.015 263 Dihedral : 31.181 153.859 865 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: -0.26 (0.69), residues: 136 helix: 0.36 (0.49), residues: 111 sheet: None (None), residues: 0 loop : -2.24 (0.85), residues: 25 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 275 TYR 0.002 0.001 TYR X 162 PHE 0.009 0.001 PHE X 187 TRP 0.036 0.005 TRP X 277 HIS 0.001 0.001 HIS X 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.16 ( 2636) covalent geometry : angle 0.64987 / 0.40 ( 3822) hydrogen bonds : bond 0.04680 / 5.08 ( 150) hydrogen bonds : angle 3.96883 / 5.43 ( 376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 638.80 seconds wall clock time: 11 minutes 35.75 seconds (695.75 seconds total)