Starting phenix.real_space_refine on Thu Jul 2 02:05:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jo3_36454/07_2026/8jo3_36454.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jo3_36454/07_2026/8jo3_36454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jo3_36454/07_2026/8jo3_36454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jo3_36454/07_2026/8jo3_36454.map" model { file = "/net/cci-nas-00/data/ceres_data/8jo3_36454/07_2026/8jo3_36454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jo3_36454/07_2026/8jo3_36454.cif" } resolution = 2.66 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= -0.002 sd= 0.151 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 S 27 5.16 5 C 3619 2.51 5 N 953 2.21 5 O 1111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 5715 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2851 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 11, 'TRANS': 338} Chain: "B" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2809 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 1.23, per 1000 atoms: 0.22 Number of scatterers: 5715 At special positions: 0 Unit cell: (64.17, 79.05, 114.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 27 16.00 P 4 15.00 O 1111 8.00 N 953 7.00 C 3619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 249.1 milliseconds 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1348 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 61.1% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 20 through 37 Processing helix chain 'A' and resid 41 through 55 removed outlier: 3.560A pdb=" N PHE A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 72 Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 77 through 91 removed outlier: 3.541A pdb=" N SER A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 118 Processing helix chain 'A' and resid 121 through 134 removed outlier: 4.280A pdb=" N PHE A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 160 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.806A pdb=" N SER A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 Processing helix chain 'A' and resid 288 through 297 removed outlier: 3.724A pdb=" N VAL A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 removed outlier: 3.537A pdb=" N ALA A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 352 Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 114 through 128 Processing helix chain 'B' and resid 139 through 147 removed outlier: 3.512A pdb=" N SER B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 198 Processing helix chain 'B' and resid 204 through 219 Processing helix chain 'B' and resid 224 through 235 Processing helix chain 'B' and resid 254 through 262 Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 263 through 264 No H-bonds generated for 'chain 'B' and resid 263 through 264' Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 288 through 298 removed outlier: 4.415A pdb=" N LYS B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASP B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 339 through 350 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.944A pdb=" N GLN B 356 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.772A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 193 Processing sheet with id=AA2, first strand: chain 'B' and resid 31 through 34 removed outlier: 6.350A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N CYS B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 74 Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA6, first strand: chain 'B' and resid 171 through 172 removed outlier: 6.603A pdb=" N ILE B 153 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N SER B 302 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU B 155 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASN B 299 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 243 320 hydrogen bonds defined for protein. 882 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1851 1.34 - 1.46: 1006 1.46 - 1.57: 2920 1.57 - 1.69: 6 1.69 - 1.81: 47 Bond restraints: 5830 Sorted by residual: bond pdb=" N ASP B 159 " pdb=" CA ASP B 159 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.56e+00 bond pdb=" N TYR B 145 " pdb=" CA TYR B 145 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.28e+00 bond pdb=" N SER B 157 " pdb=" CA SER B 157 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.27e-02 6.20e+03 4.63e+00 bond pdb=" N GLY B 158 " pdb=" CA GLY B 158 " ideal model delta sigma weight residual 1.449 1.476 -0.027 1.45e-02 4.76e+03 3.51e+00 bond pdb=" N ASP B 156 " pdb=" CA ASP B 156 " ideal model delta sigma weight residual 1.463 1.487 -0.025 1.37e-02 5.33e+03 3.23e+00 ... (remaining 5825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 7781 1.90 - 3.79: 98 3.79 - 5.69: 17 5.69 - 7.58: 0 7.58 - 9.48: 3 Bond angle restraints: 7899 Sorted by residual: angle pdb=" C1' AMP A 501 " pdb=" C2' AMP A 501 " pdb=" C3' AMP A 501 " ideal model delta sigma weight residual 111.00 101.63 9.37 3.00e+00 1.11e-01 9.76e+00 angle pdb=" CA ASP B 156 " pdb=" C ASP B 156 " pdb=" O ASP B 156 " ideal model delta sigma weight residual 121.39 118.26 3.13 1.12e+00 7.97e-01 7.82e+00 angle pdb=" C2' AMP A 501 " pdb=" C3' AMP A 501 " pdb=" C4' AMP A 501 " ideal model delta sigma weight residual 111.00 102.85 8.15 3.00e+00 1.11e-01 7.37e+00 angle pdb=" CA SER B 157 " pdb=" C SER B 157 " pdb=" O SER B 157 " ideal model delta sigma weight residual 120.54 118.12 2.42 1.04e+00 9.25e-01 5.40e+00 angle pdb=" C GLY A 227 " pdb=" N GLY A 228 " pdb=" CA GLY A 228 " ideal model delta sigma weight residual 120.10 122.24 -2.14 9.50e-01 1.11e+00 5.08e+00 ... (remaining 7894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.44: 3247 26.44 - 52.88: 272 52.88 - 79.32: 43 79.32 - 105.76: 5 105.76 - 132.20: 1 Dihedral angle restraints: 3568 sinusoidal: 1479 harmonic: 2089 Sorted by residual: dihedral pdb=" C5' AMP A 501 " pdb=" O5' AMP A 501 " pdb=" P AMP A 501 " pdb=" O3P AMP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 167.80 132.20 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" CA PHE A 238 " pdb=" C PHE A 238 " pdb=" N VAL A 239 " pdb=" CA VAL A 239 " ideal model delta harmonic sigma weight residual 180.00 162.05 17.95 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CG ARG B 337 " pdb=" CD ARG B 337 " pdb=" NE ARG B 337 " pdb=" CZ ARG B 337 " ideal model delta sinusoidal sigma weight residual 180.00 137.78 42.22 2 1.50e+01 4.44e-03 9.63e+00 ... (remaining 3565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 683 0.046 - 0.092: 156 0.092 - 0.139: 44 0.139 - 0.185: 1 0.185 - 0.231: 1 Chirality restraints: 885 Sorted by residual: chirality pdb=" C3' AMP A 501 " pdb=" C2' AMP A 501 " pdb=" C4' AMP A 501 " pdb=" O3' AMP A 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB THR A 331 " pdb=" CA THR A 331 " pdb=" OG1 THR A 331 " pdb=" CG2 THR A 331 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CB ILE B 252 " pdb=" CA ILE B 252 " pdb=" CG1 ILE B 252 " pdb=" CG2 ILE B 252 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 882 not shown) Planarity restraints: 1005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 211 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO A 212 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 323 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO B 324 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 324 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 324 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 333 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO B 334 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 334 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 334 " -0.016 5.00e-02 4.00e+02 ... (remaining 1002 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 417 2.74 - 3.28: 5786 3.28 - 3.82: 10492 3.82 - 4.36: 12799 4.36 - 4.90: 21407 Nonbonded interactions: 50901 Sorted by model distance: nonbonded pdb=" OH TYR A 108 " pdb=" O ALA A 315 " model vdw 2.196 3.040 nonbonded pdb=" OE1 GLU A 343 " pdb=" OG1 THR B 353 " model vdw 2.204 3.040 nonbonded pdb=" O LEU A 158 " pdb=" N6 AMP A 501 " model vdw 2.251 3.120 nonbonded pdb=" O SER B 35 " pdb=" OG SER B 35 " model vdw 2.273 3.040 nonbonded pdb=" O ILE A 25 " pdb=" OG1 THR A 29 " model vdw 2.275 3.040 ... (remaining 50896 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.390 Find NCS groups from input model: 0.040 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:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.003 0.036 5830 Z= 0.149 Angle : 0.557 9.477 7899 Z= 0.283 Chirality : 0.042 0.231 885 Planarity : 0.004 0.050 1005 Dihedral : 18.830 132.198 2220 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.56 % Allowed : 23.56 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.33), residues: 703 helix: 1.68 (0.27), residues: 375 sheet: 0.01 (0.57), residues: 77 loop : 0.97 (0.45), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.011 0.001 TYR A 42 PHE 0.014 0.001 PHE A 125 TRP 0.009 0.002 TRP A 277 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 5830) covalent geometry : angle 0.55689 / 0.28 ( 7899) hydrogen bonds : bond 0.12821 / 8.25 ( 318) hydrogen bonds : angle 6.26122 / 4.41 ( 882) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.226 Fit side-chains REVERT: A 92 THR cc_start: 0.8263 (m) cc_final: 0.8061 (p) REVERT: B 83 ASP cc_start: 0.8103 (m-30) cc_final: 0.7754 (m-30) outliers start: 16 outliers final: 15 residues processed: 108 average time/residue: 0.5261 time to fit residues: 59.5655 Evaluate side-chains 105 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 241 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 GLN A 148 ASN A 272 ASN A 332 GLN B 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.152506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.123725 restraints weight = 5768.716| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.40 r_work: 0.3270 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5830 Z= 0.138 Angle : 0.531 6.481 7899 Z= 0.269 Chirality : 0.042 0.138 885 Planarity : 0.004 0.050 1005 Dihedral : 9.217 126.388 835 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.88 % Allowed : 20.51 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.33), residues: 703 helix: 1.66 (0.27), residues: 379 sheet: 0.16 (0.56), residues: 80 loop : 1.06 (0.46), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 256 TYR 0.013 0.001 TYR A 42 PHE 0.015 0.001 PHE A 125 TRP 0.008 0.002 TRP A 277 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 5830) covalent geometry : angle 0.53107 / 0.27 ( 7899) hydrogen bonds : bond 0.04046 / 2.59 ( 318) hydrogen bonds : angle 4.97305 / 3.47 ( 882) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.226 Fit side-chains REVERT: A 187 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6645 (tm-30) REVERT: B 74 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6664 (pp20) REVERT: B 97 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7080 (mtp180) outliers start: 18 outliers final: 6 residues processed: 105 average time/residue: 0.5910 time to fit residues: 64.5532 Evaluate side-chains 98 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 288 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN B 75 HIS B 94 ASN B 355 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.151195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.122077 restraints weight = 5693.423| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.38 r_work: 0.3298 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5830 Z= 0.132 Angle : 0.518 6.775 7899 Z= 0.262 Chirality : 0.042 0.132 885 Planarity : 0.004 0.050 1005 Dihedral : 7.968 102.405 815 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.37 % Allowed : 21.47 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.33), residues: 703 helix: 1.61 (0.27), residues: 386 sheet: 0.18 (0.54), residues: 80 loop : 1.08 (0.46), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 185 TYR 0.013 0.001 TYR A 42 PHE 0.014 0.001 PHE A 125 TRP 0.008 0.001 TRP A 277 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 5830) covalent geometry : angle 0.51763 / 0.26 ( 7899) hydrogen bonds : bond 0.03865 / 2.45 ( 318) hydrogen bonds : angle 4.75924 / 3.31 ( 882) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: B 74 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6611 (pp20) outliers start: 21 outliers final: 7 residues processed: 109 average time/residue: 0.6079 time to fit residues: 69.2106 Evaluate side-chains 98 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN B 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.153109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.125171 restraints weight = 5734.314| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.32 r_work: 0.3286 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5830 Z= 0.157 Angle : 0.535 6.940 7899 Z= 0.271 Chirality : 0.043 0.136 885 Planarity : 0.004 0.050 1005 Dihedral : 7.851 86.479 814 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.37 % Allowed : 21.31 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.33), residues: 703 helix: 1.53 (0.27), residues: 386 sheet: 0.06 (0.54), residues: 80 loop : 1.10 (0.46), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 185 TYR 0.014 0.001 TYR A 42 PHE 0.016 0.001 PHE A 125 TRP 0.008 0.002 TRP A 277 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 5830) covalent geometry : angle 0.53499 / 0.27 ( 7899) hydrogen bonds : bond 0.03970 / 2.51 ( 318) hydrogen bonds : angle 4.70202 / 3.25 ( 882) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6481 (tm-30) REVERT: B 74 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6527 (pp20) outliers start: 21 outliers final: 11 residues processed: 109 average time/residue: 0.6383 time to fit residues: 72.5381 Evaluate side-chains 105 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN B 94 ASN B 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.147903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.118205 restraints weight = 5828.262| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.41 r_work: 0.3248 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5830 Z= 0.202 Angle : 0.574 7.027 7899 Z= 0.294 Chirality : 0.045 0.165 885 Planarity : 0.004 0.051 1005 Dihedral : 7.852 75.051 814 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.65 % Allowed : 20.35 % Favored : 75.00 % 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: 1.56 (0.33), residues: 703 helix: 1.43 (0.27), residues: 383 sheet: -0.13 (0.53), residues: 80 loop : 1.07 (0.46), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 185 TYR 0.015 0.002 TYR A 42 PHE 0.017 0.002 PHE A 125 TRP 0.010 0.002 TRP A 277 HIS 0.005 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 ( 5830) covalent geometry : angle 0.57444 / 0.29 ( 7899) hydrogen bonds : bond 0.04346 / 2.74 ( 318) hydrogen bonds : angle 4.79619 / 3.31 ( 882) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: A 223 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6857 (mm-30) REVERT: B 74 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6573 (pp20) outliers start: 29 outliers final: 11 residues processed: 111 average time/residue: 0.6115 time to fit residues: 70.9005 Evaluate side-chains 105 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 315 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 3 optimal weight: 0.0870 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.0470 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN B 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.155500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.128791 restraints weight = 5766.354| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.34 r_work: 0.3292 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5830 Z= 0.115 Angle : 0.506 6.574 7899 Z= 0.257 Chirality : 0.042 0.165 885 Planarity : 0.004 0.049 1005 Dihedral : 7.196 63.549 814 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.69 % Allowed : 21.96 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.33), residues: 703 helix: 1.70 (0.27), residues: 381 sheet: 0.16 (0.54), residues: 79 loop : 1.03 (0.45), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 185 TYR 0.013 0.001 TYR A 42 PHE 0.011 0.001 PHE A 125 TRP 0.010 0.001 TRP A 277 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 5830) covalent geometry : angle 0.50603 / 0.26 ( 7899) hydrogen bonds : bond 0.03648 / 2.31 ( 318) hydrogen bonds : angle 4.50426 / 3.10 ( 882) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.8086 (mp) REVERT: A 347 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7316 (ptmt) REVERT: B 74 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6593 (pp20) REVERT: B 97 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7169 (mtp180) outliers start: 23 outliers final: 11 residues processed: 113 average time/residue: 0.5571 time to fit residues: 65.8204 Evaluate side-chains 107 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 315 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 ASN A 82 GLN A 148 ASN A 272 ASN B 94 ASN B 355 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.150669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.121187 restraints weight = 5771.857| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.42 r_work: 0.3288 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5830 Z= 0.140 Angle : 0.524 6.567 7899 Z= 0.266 Chirality : 0.042 0.147 885 Planarity : 0.004 0.050 1005 Dihedral : 7.115 61.256 814 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.37 % Allowed : 22.76 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.33), residues: 703 helix: 1.55 (0.27), residues: 387 sheet: 0.04 (0.54), residues: 80 loop : 1.03 (0.46), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 185 TYR 0.014 0.001 TYR A 42 PHE 0.015 0.001 PHE A 125 TRP 0.009 0.002 TRP A 277 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 5830) covalent geometry : angle 0.52379 / 0.27 ( 7899) hydrogen bonds : bond 0.03822 / 2.42 ( 318) hydrogen bonds : angle 4.53296 / 3.12 ( 882) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6971 (mm-30) REVERT: A 295 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8165 (mp) REVERT: A 347 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7385 (ptmt) REVERT: B 74 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6593 (pp20) REVERT: B 97 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7202 (mtp180) REVERT: B 185 ARG cc_start: 0.7752 (tpp80) cc_final: 0.7504 (tpp80) outliers start: 21 outliers final: 13 residues processed: 110 average time/residue: 0.5662 time to fit residues: 65.0760 Evaluate side-chains 111 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 315 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 0.2980 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 ASN B 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.151040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.121743 restraints weight = 5739.877| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.40 r_work: 0.3298 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5830 Z= 0.136 Angle : 0.523 6.553 7899 Z= 0.265 Chirality : 0.042 0.150 885 Planarity : 0.004 0.050 1005 Dihedral : 7.005 60.357 814 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.21 % Allowed : 22.92 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.33), residues: 703 helix: 1.56 (0.27), residues: 387 sheet: 0.14 (0.53), residues: 79 loop : 1.00 (0.46), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 185 TYR 0.014 0.001 TYR A 42 PHE 0.014 0.001 PHE A 125 TRP 0.009 0.001 TRP A 277 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 5830) covalent geometry : angle 0.52280 / 0.26 ( 7899) hydrogen bonds : bond 0.03778 / 2.40 ( 318) hydrogen bonds : angle 4.51707 / 3.10 ( 882) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6963 (mm-30) REVERT: A 295 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8167 (mp) REVERT: A 347 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7379 (ptmt) REVERT: B 74 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6569 (pp20) REVERT: B 97 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7186 (mtp180) outliers start: 20 outliers final: 11 residues processed: 108 average time/residue: 0.5593 time to fit residues: 63.0623 Evaluate side-chains 109 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 315 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 39 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 94 ASN B 355 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.152158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.122999 restraints weight = 5784.753| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.40 r_work: 0.3337 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5830 Z= 0.120 Angle : 0.515 6.429 7899 Z= 0.261 Chirality : 0.042 0.147 885 Planarity : 0.004 0.049 1005 Dihedral : 6.852 59.717 814 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.69 % Allowed : 22.76 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.33), residues: 703 helix: 1.61 (0.27), residues: 387 sheet: 0.19 (0.54), residues: 79 loop : 0.99 (0.45), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 185 TYR 0.014 0.001 TYR A 42 PHE 0.013 0.001 PHE A 125 TRP 0.009 0.001 TRP A 277 HIS 0.006 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 5830) covalent geometry : angle 0.51507 / 0.26 ( 7899) hydrogen bonds : bond 0.03622 / 2.30 ( 318) hydrogen bonds : angle 4.43416 / 3.04 ( 882) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: A 187 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6387 (tm-30) REVERT: A 223 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: A 295 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8127 (mp) REVERT: A 347 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7338 (ptmt) REVERT: B 74 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6576 (pp20) REVERT: B 97 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7153 (mtp180) outliers start: 23 outliers final: 10 residues processed: 112 average time/residue: 0.6045 time to fit residues: 70.6546 Evaluate side-chains 109 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 315 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN B 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.150741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.121369 restraints weight = 5821.275| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.41 r_work: 0.3289 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5830 Z= 0.147 Angle : 0.543 6.383 7899 Z= 0.278 Chirality : 0.043 0.159 885 Planarity : 0.004 0.050 1005 Dihedral : 7.014 59.635 814 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.72 % Allowed : 24.04 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.33), residues: 703 helix: 1.52 (0.27), residues: 387 sheet: 0.25 (0.56), residues: 73 loop : 0.97 (0.45), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 185 TYR 0.014 0.001 TYR A 42 PHE 0.014 0.001 PHE A 125 TRP 0.008 0.002 TRP A 277 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 5830) covalent geometry : angle 0.54325 / 0.28 ( 7899) hydrogen bonds : bond 0.03880 / 2.47 ( 318) hydrogen bonds : angle 4.52332 / 3.11 ( 882) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 187 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6404 (tm-30) REVERT: A 223 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6973 (mm-30) REVERT: A 295 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8169 (mp) REVERT: A 347 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7369 (ptmt) REVERT: B 74 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6602 (pp20) REVERT: B 97 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7177 (mtp180) REVERT: B 119 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7529 (mt-10) outliers start: 17 outliers final: 10 residues processed: 105 average time/residue: 0.6222 time to fit residues: 68.1522 Evaluate side-chains 109 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 315 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 63 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN B 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.151584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122568 restraints weight = 5718.796| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.39 r_work: 0.3283 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5830 Z= 0.159 Angle : 0.556 6.271 7899 Z= 0.285 Chirality : 0.044 0.165 885 Planarity : 0.004 0.050 1005 Dihedral : 7.257 60.149 814 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.88 % Allowed : 23.88 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.33), residues: 703 helix: 1.46 (0.27), residues: 386 sheet: 0.23 (0.56), residues: 73 loop : 0.99 (0.45), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 185 TYR 0.015 0.001 TYR A 42 PHE 0.015 0.001 PHE A 125 TRP 0.008 0.002 TRP A 277 HIS 0.006 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 5830) covalent geometry : angle 0.55632 / 0.29 ( 7899) hydrogen bonds : bond 0.03993 / 2.54 ( 318) hydrogen bonds : angle 4.60518 / 3.17 ( 882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2303.57 seconds wall clock time: 40 minutes 9.04 seconds (2409.04 seconds total)