Starting phenix.real_space_refine on Tue Aug 4 17:51:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jo3_36454/08_2026/8jo3_36454.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jo3_36454/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jo3_36454/08_2026/8jo3_36454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jo3_36454/08_2026/8jo3_36454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jo3_36454/08_2026/8jo3_36454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jo3_36454/08_2026/8jo3_36454.map" } 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-2.2rc3-6140/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, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.99, per 1000 atoms: 0.17 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: 0.58 Conformation dependent library (CDL) restraints added in 196.7 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: 0.29 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: 0.88 Time building geometry restraints manager: 0.79 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: 7791 1.90 - 3.79: 93 3.79 - 5.69: 14 5.69 - 7.58: 0 7.58 - 9.48: 1 Bond angle restraints: 7899 Sorted by residual: 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=" 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 angle pdb=" O TYR B 145 " pdb=" C TYR B 145 " pdb=" N ALA B 146 " ideal model delta sigma weight residual 122.12 124.15 -2.03 1.06e+00 8.90e-01 3.65e+00 angle pdb=" N TYR B 145 " pdb=" CA TYR B 145 " pdb=" C TYR B 145 " ideal model delta sigma weight residual 111.28 109.22 2.06 1.09e+00 8.42e-01 3.56e+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 - 0.031: 536 0.031 - 0.062: 237 0.062 - 0.092: 66 0.092 - 0.123: 45 0.123 - 0.154: 1 Chirality restraints: 885 Sorted by residual: 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 chirality pdb=" CA VAL B 19 " pdb=" N VAL B 19 " pdb=" C VAL B 19 " pdb=" CB VAL B 19 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.66e-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: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.440 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.440 ------------------------------------------------------------------------------- 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= 0.145 Angle : 0.527 9.477 7899 Z= 0.277 Chirality : 0.041 0.154 885 Planarity : 0.004 0.050 1005 Dihedral : 18.818 132.198 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 0.00298 / 0.15 ( 5830) covalent geometry : angle 0.52688 / 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 : 0.223 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: 0.5064 time to fit residues: 57.3565 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 : 0.213 ------------------------------------------------------------------------------- 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 = 0.152572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123819 restraints weight = 5767.456| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.40 r_work: 0.3275 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.0729 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= 0.137 Angle : 0.523 6.554 7899 Z= 0.267 Chirality : 0.042 0.130 885 Planarity : 0.004 0.050 1005 Dihedral : 9.290 126.014 835 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.59 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: 0.15 (0.55), residues: 80 loop : 1.05 (0.46), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 136 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 0.00313 / 0.14 ( 5830) covalent geometry : angle 0.52261 / 0.27 ( 7899) hydrogen bonds : bond 0.03982 / 2.55 ( 318) hydrogen bonds : angle 4.95406 / 3.46 ( 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 114 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.221 Fit side-chains REVERT: A 187 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6645 (tm-30) REVERT: B 74 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6657 (pp20) REVERT: B 97 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7069 (mtp180) outliers start: 18 outliers final: 6 residues processed: 106 average time/residue: 0.6192 time to fit residues: 68.4217 Evaluate side-chains 99 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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: 0.3980 chunk 2 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.152001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.122943 restraints weight = 5686.860| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.39 r_work: 0.3292 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0950 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= 0.122 Angle : 0.502 6.612 7899 Z= 0.256 Chirality : 0.041 0.130 885 Planarity : 0.004 0.050 1005 Dihedral : 8.086 109.004 815 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.69 % Allowed : 20.67 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.33), residues: 703 helix: 1.69 (0.27), residues: 380 sheet: 0.20 (0.55), residues: 80 loop : 1.10 (0.46), residues: 243 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 0.013 0.001 PHE A 125 TRP 0.009 0.001 TRP A 277 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 5830) covalent geometry : angle 0.50225 / 0.26 ( 7899) hydrogen bonds : bond 0.03752 / 2.38 ( 318) hydrogen bonds : angle 4.71349 / 3.28 ( 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 120 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: B 185 ARG cc_start: 0.7729 (tpp80) cc_final: 0.7375 (tpp80) outliers start: 23 outliers final: 8 residues processed: 111 average time/residue: 0.5736 time to fit residues: 66.4696 Evaluate side-chains 99 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.163 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 ASP 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: 1.9990 chunk 64 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.152540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124549 restraints weight = 5745.493| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.32 r_work: 0.3301 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5830 Z= 0.174 Angle : 0.540 6.724 7899 Z= 0.276 Chirality : 0.043 0.136 885 Planarity : 0.004 0.051 1005 Dihedral : 8.015 97.762 814 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.21 % Allowed : 21.47 % 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: 1.69 (0.33), residues: 703 helix: 1.50 (0.27), residues: 385 sheet: 0.02 (0.53), residues: 80 loop : 1.16 (0.46), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 30 TYR 0.014 0.001 TYR A 42 PHE 0.017 0.002 PHE A 125 TRP 0.009 0.002 TRP A 277 HIS 0.005 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 ( 5830) covalent geometry : angle 0.53977 / 0.28 ( 7899) hydrogen bonds : bond 0.04104 / 2.59 ( 318) hydrogen bonds : angle 4.74159 / 3.28 ( 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: 20 poor density : 96 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6489 (tm-30) REVERT: B 119 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7594 (mt-10) REVERT: B 185 ARG cc_start: 0.7748 (tpp80) cc_final: 0.7472 (tpp80) outliers start: 20 outliers final: 9 residues processed: 108 average time/residue: 0.5918 time to fit residues: 66.6941 Evaluate side-chains 101 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 ASP 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: 6.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.150291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.120796 restraints weight = 5819.792| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.41 r_work: 0.3282 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5830 Z= 0.148 Angle : 0.523 6.729 7899 Z= 0.269 Chirality : 0.042 0.172 885 Planarity : 0.004 0.050 1005 Dihedral : 7.868 93.101 814 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.37 % Allowed : 21.96 % Favored : 74.68 % 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: 1.52 (0.27), residues: 386 sheet: 0.04 (0.53), residues: 80 loop : 1.12 (0.46), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 30 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 0.00344 / 0.15 ( 5830) covalent geometry : angle 0.52291 / 0.27 ( 7899) hydrogen bonds : bond 0.03941 / 2.49 ( 318) hydrogen bonds : angle 4.64384 / 3.21 ( 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 115 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6519 (tm-30) REVERT: B 119 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7619 (mt-10) REVERT: B 185 ARG cc_start: 0.7797 (tpp80) cc_final: 0.7491 (tpp80) outliers start: 21 outliers final: 9 residues processed: 108 average time/residue: 0.6045 time to fit residues: 68.1508 Evaluate side-chains 102 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 321 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 3 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 148 ASN B 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.149723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.120171 restraints weight = 5782.663| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.42 r_work: 0.3273 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1081 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= 0.156 Angle : 0.532 6.754 7899 Z= 0.274 Chirality : 0.043 0.165 885 Planarity : 0.004 0.050 1005 Dihedral : 7.830 87.624 814 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.01 % Allowed : 21.79 % Favored : 74.20 % 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: 1.65 (0.33), residues: 703 helix: 1.50 (0.27), residues: 386 sheet: 0.00 (0.54), residues: 80 loop : 1.08 (0.46), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 30 TYR 0.014 0.001 TYR A 42 PHE 0.016 0.001 PHE A 125 TRP 0.009 0.002 TRP A 277 HIS 0.004 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 5830) covalent geometry : angle 0.53203 / 0.27 ( 7899) hydrogen bonds : bond 0.03997 / 2.53 ( 318) hydrogen bonds : angle 4.62958 / 3.19 ( 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: 25 poor density : 96 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6552 (tm-30) REVERT: A 223 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6960 (mm-30) REVERT: B 97 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7185 (mtp180) REVERT: B 119 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7609 (mt-10) outliers start: 25 outliers final: 14 residues processed: 112 average time/residue: 0.5805 time to fit residues: 67.8003 Evaluate side-chains 108 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 23 ASP 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 7 THR 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: 0.9990 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 ASN A 82 GLN A 148 ASN B 94 ASN B 355 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.150790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121536 restraints weight = 5763.187| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.41 r_work: 0.3318 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1136 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= 0.135 Angle : 0.517 6.757 7899 Z= 0.266 Chirality : 0.042 0.154 885 Planarity : 0.004 0.049 1005 Dihedral : 7.752 84.771 814 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 4.01 % Allowed : 22.12 % 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: 1.67 (0.33), residues: 703 helix: 1.52 (0.27), residues: 387 sheet: 0.13 (0.54), residues: 79 loop : 1.00 (0.46), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 5830) covalent geometry : angle 0.51709 / 0.27 ( 7899) hydrogen bonds : bond 0.03839 / 2.43 ( 318) hydrogen bonds : angle 4.55294 / 3.13 ( 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 120 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: A 223 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6957 (mm-30) REVERT: A 295 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8133 (mp) REVERT: A 347 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7349 (ptmt) REVERT: B 97 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7185 (mtp180) REVERT: B 119 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7607 (mt-10) REVERT: B 185 ARG cc_start: 0.7690 (tpp80) cc_final: 0.7397 (tpp80) outliers start: 25 outliers final: 14 residues processed: 111 average time/residue: 0.6216 time to fit residues: 72.0825 Evaluate side-chains 113 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 78 THR 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 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 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: 0.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 148 ASN A 272 ASN B 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.151686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122718 restraints weight = 5723.804| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.40 r_work: 0.3293 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5830 Z= 0.148 Angle : 0.529 6.767 7899 Z= 0.272 Chirality : 0.043 0.156 885 Planarity : 0.004 0.050 1005 Dihedral : 7.741 80.358 814 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.37 % Allowed : 23.24 % Favored : 73.40 % 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: 1.61 (0.33), residues: 703 helix: 1.49 (0.27), residues: 386 sheet: 0.03 (0.53), residues: 79 loop : 1.00 (0.46), residues: 238 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 0.015 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 0.00345 / 0.15 ( 5830) covalent geometry : angle 0.52914 / 0.27 ( 7899) hydrogen bonds : bond 0.03928 / 2.49 ( 318) hydrogen bonds : angle 4.57652 / 3.15 ( 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 114 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6556 (tm-30) REVERT: A 223 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6932 (mm-30) REVERT: A 347 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7377 (ptmt) REVERT: B 97 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7157 (mtp180) REVERT: B 119 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 185 ARG cc_start: 0.7740 (tpp80) cc_final: 0.7365 (tpp80) outliers start: 21 outliers final: 13 residues processed: 106 average time/residue: 0.5316 time to fit residues: 58.9472 Evaluate side-chains 109 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 23 ASP 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 321 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 7 THR 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: 0.9990 chunk 66 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.0000 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.154258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.126693 restraints weight = 5756.105| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.32 r_work: 0.3351 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1144 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= 0.135 Angle : 0.522 6.744 7899 Z= 0.268 Chirality : 0.042 0.154 885 Planarity : 0.004 0.049 1005 Dihedral : 7.652 77.682 814 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.04 % Allowed : 23.88 % Favored : 73.08 % 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: 1.64 (0.33), residues: 703 helix: 1.53 (0.27), residues: 387 sheet: 0.04 (0.53), residues: 79 loop : 0.96 (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 0.005 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 5830) covalent geometry : angle 0.52222 / 0.27 ( 7899) hydrogen bonds : bond 0.03820 / 2.42 ( 318) hydrogen bonds : angle 4.53204 / 3.12 ( 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 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6955 (mm-30) REVERT: A 347 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7333 (ptmt) REVERT: B 97 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7190 (mtp180) REVERT: B 119 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7595 (mt-10) outliers start: 19 outliers final: 11 residues processed: 105 average time/residue: 0.5894 time to fit residues: 64.6114 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 : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 36 LEU 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 321 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 7 THR 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: 0.7980 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.153654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126072 restraints weight = 5786.531| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.30 r_work: 0.3303 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1161 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 : 0.536 6.758 7899 Z= 0.276 Chirality : 0.043 0.155 885 Planarity : 0.004 0.050 1005 Dihedral : 7.724 73.181 814 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.56 % Allowed : 24.36 % Favored : 73.08 % 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: 1.58 (0.33), residues: 703 helix: 1.49 (0.27), residues: 387 sheet: -0.12 (0.53), residues: 80 loop : 0.99 (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 0.004 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 5830) covalent geometry : angle 0.53628 / 0.28 ( 7899) hydrogen bonds : bond 0.03909 / 2.48 ( 318) hydrogen bonds : angle 4.56049 / 3.14 ( 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 109 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7005 (mm-30) REVERT: A 347 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7402 (ptmt) REVERT: B 97 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7179 (mtp180) REVERT: B 119 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7594 (mt-10) REVERT: B 185 ARG cc_start: 0.7709 (tpp80) cc_final: 0.7469 (tpp80) outliers start: 16 outliers final: 12 residues processed: 104 average time/residue: 0.6260 time to fit residues: 67.9012 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 : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 36 LEU 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 321 ASP Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 7 THR 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: 3.9990 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.0370 chunk 6 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 148 ASN B 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.154992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128319 restraints weight = 5704.553| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.30 r_work: 0.3284 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.003 0.042 5830 Z= 0.128 Angle : 0.527 6.678 7899 Z= 0.272 Chirality : 0.042 0.156 885 Planarity : 0.004 0.049 1005 Dihedral : 7.602 70.110 814 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.56 % Allowed : 24.20 % 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: 1.53 (0.27), residues: 387 sheet: 0.02 (0.54), residues: 79 loop : 0.96 (0.46), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 185 TYR 0.015 0.001 TYR A 256 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 0.00295 / 0.13 ( 5830) covalent geometry : angle 0.52718 / 0.27 ( 7899) hydrogen bonds : bond 0.03761 / 2.39 ( 318) hydrogen bonds : angle 4.52811 / 3.11 ( 882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2287.72 seconds wall clock time: 39 minutes 44.44 seconds (2384.44 seconds total)