Starting phenix.real_space_refine on Fri Aug 22 16:14:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jo3_36454/08_2025/8jo3_36454.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jo3_36454/08_2025/8jo3_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_2025/8jo3_36454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jo3_36454/08_2025/8jo3_36454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jo3_36454/08_2025/8jo3_36454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jo3_36454/08_2025/8jo3_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-2.0-5787/lib/python3.9/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: 1.46, per 1000 atoms: 0.26 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: 0.36 Conformation dependent library (CDL) restraints added in 171.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.73 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.230 Find NCS groups from input model: 0.030 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 aren 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 covalent geometry : bond 0.00305 ( 5830) covalent geometry : angle 0.55689 ( 7899) hydrogen bonds : bond 0.12821 ( 318) hydrogen bonds : angle 6.26122 ( 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 : 0.194 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: 0.4814 time to fit residues: 54.3074 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 : 0.190 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 148 ASN A 272 ASN A 300 HIS A 332 GLN B 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.152464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123715 restraints weight = 5774.386| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.40 r_work: 0.3272 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.0703 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 : 0.531 6.298 7899 Z= 0.268 Chirality : 0.042 0.138 885 Planarity : 0.004 0.050 1005 Dihedral : 9.421 129.153 835 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.88 % Allowed : 21.31 % Favored : 75.80 % 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 aren 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 102 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 covalent geometry : bond 0.00313 ( 5830) covalent geometry : angle 0.53058 ( 7899) hydrogen bonds : bond 0.04095 ( 318) hydrogen bonds : angle 4.99721 ( 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 : 0.257 Fit side-chains REVERT: A 187 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6637 (tm-30) REVERT: B 74 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6666 (pp20) REVERT: B 97 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7097 (mtp180) outliers start: 18 outliers final: 6 residues processed: 106 average time/residue: 0.6218 time to fit residues: 68.6070 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 : 0.155 ------------------------------------------------------------------------------- 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: 0.4980 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 300 HIS B 75 HIS 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 = 0.3661 r_free = 0.3661 target = 0.150007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.120762 restraints weight = 5687.916| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.38 r_work: 0.3299 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5830 Z= 0.151 Angle : 0.534 6.801 7899 Z= 0.270 Chirality : 0.043 0.136 885 Planarity : 0.004 0.050 1005 Dihedral : 8.141 102.812 815 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.53 % Allowed : 21.47 % 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 aren not related in a simple way. whole: 1.71 (0.33), residues: 703 helix: 1.54 (0.27), residues: 386 sheet: 0.09 (0.54), residues: 80 loop : 1.09 (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 0.015 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 covalent geometry : bond 0.00350 ( 5830) covalent geometry : angle 0.53367 ( 7899) hydrogen bonds : bond 0.04029 ( 318) hydrogen bonds : angle 4.83654 ( 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 115 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6656 (tm-30) REVERT: B 74 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6662 (pp20) REVERT: B 97 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7080 (mtp180) outliers start: 22 outliers final: 9 residues processed: 107 average time/residue: 0.6384 time to fit residues: 71.3022 Evaluate side-chains 100 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 36 LEU 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 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 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: 0.6980 chunk 2 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3713 r_free = 0.3713 target = 0.154119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.126394 restraints weight = 5740.562| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.32 r_work: 0.3300 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.0993 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= 0.136 Angle : 0.517 6.855 7899 Z= 0.262 Chirality : 0.042 0.130 885 Planarity : 0.004 0.050 1005 Dihedral : 7.890 90.110 814 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.37 % Allowed : 21.15 % Favored : 75.48 % 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 aren not related in a simple way. whole: 1.73 (0.33), residues: 703 helix: 1.56 (0.27), residues: 386 sheet: 0.09 (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 0.014 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 covalent geometry : bond 0.00312 ( 5830) covalent geometry : angle 0.51748 ( 7899) hydrogen bonds : bond 0.03826 ( 318) hydrogen bonds : angle 4.66612 ( 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 115 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6630 (tm-30) REVERT: B 74 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6607 (pp20) REVERT: B 97 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7101 (mtp180) outliers start: 21 outliers final: 10 residues processed: 107 average time/residue: 0.5960 time to fit residues: 66.5641 Evaluate side-chains 104 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 97 ARG 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: 2.9990 chunk 53 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 300 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 = 0.3629 r_free = 0.3629 target = 0.146997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117110 restraints weight = 5825.445| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.42 r_work: 0.3070 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 5830 Z= 0.235 Angle : 0.599 7.082 7899 Z= 0.307 Chirality : 0.046 0.175 885 Planarity : 0.004 0.051 1005 Dihedral : 8.181 78.114 814 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.33 % Allowed : 21.31 % 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 aren not related in a simple way. whole: 1.47 (0.33), residues: 703 helix: 1.33 (0.27), residues: 383 sheet: -0.05 (0.55), residues: 73 loop : 1.00 (0.45), residues: 247 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 0.011 0.002 TRP A 277 HIS 0.007 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 5830) covalent geometry : angle 0.59931 ( 7899) hydrogen bonds : bond 0.04555 ( 318) hydrogen bonds : angle 4.88455 ( 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 120 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6587 (tm-30) REVERT: A 223 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6826 (mm-30) REVERT: B 74 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6394 (pp20) REVERT: B 97 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7141 (mtp180) outliers start: 27 outliers final: 9 residues processed: 109 average time/residue: 0.6454 time to fit residues: 73.2216 Evaluate side-chains 102 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.4980 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3683 r_free = 0.3683 target = 0.151510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122464 restraints weight = 5804.402| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.41 r_work: 0.3309 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1110 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= 0.144 Angle : 0.530 6.779 7899 Z= 0.270 Chirality : 0.043 0.167 885 Planarity : 0.004 0.049 1005 Dihedral : 7.681 68.308 814 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.85 % Allowed : 22.28 % 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 aren not related in a simple way. whole: 1.60 (0.33), residues: 703 helix: 1.49 (0.27), residues: 386 sheet: -0.10 (0.54), residues: 80 loop : 1.04 (0.46), 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 0.014 0.001 PHE A 125 TRP 0.010 0.002 TRP A 277 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5830) covalent geometry : angle 0.53027 ( 7899) hydrogen bonds : bond 0.03933 ( 318) hydrogen bonds : angle 4.63795 ( 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: 24 poor density : 97 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6669 (tm-30) REVERT: B 74 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6537 (pp20) REVERT: B 97 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7154 (mtp180) outliers start: 24 outliers final: 12 residues processed: 113 average time/residue: 0.5683 time to fit residues: 67.0039 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 : 0.314 ------------------------------------------------------------------------------- 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 134 GLU Chi-restraints excluded: chain A residue 187 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 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 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: 2.9990 chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 272 ASN 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 = 0.3661 r_free = 0.3661 target = 0.149831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.120473 restraints weight = 5770.444| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.41 r_work: 0.3308 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5830 Z= 0.149 Angle : 0.537 6.653 7899 Z= 0.274 Chirality : 0.043 0.161 885 Planarity : 0.004 0.049 1005 Dihedral : 7.518 63.270 814 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 4.01 % Allowed : 21.96 % Favored : 74.04 % 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 aren not related in a simple way. whole: 1.62 (0.33), residues: 703 helix: 1.48 (0.27), residues: 386 sheet: 0.07 (0.56), residues: 73 loop : 0.97 (0.45), residues: 244 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 covalent geometry : bond 0.00347 ( 5830) covalent geometry : angle 0.53732 ( 7899) hydrogen bonds : bond 0.03974 ( 318) hydrogen bonds : angle 4.61190 ( 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 121 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6673 (tm-30) REVERT: A 223 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6993 (mm-30) REVERT: A 347 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7403 (ptmt) REVERT: B 74 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6583 (pp20) REVERT: B 97 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7144 (mtp180) REVERT: B 185 ARG cc_start: 0.7751 (tpp80) cc_final: 0.7511 (tpp80) outliers start: 25 outliers final: 15 residues processed: 112 average time/residue: 0.6122 time to fit residues: 71.5615 Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 261 LYS 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 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 Chi-restraints excluded: chain B residue 346 SER 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: 0.7980 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 82 GLN A 148 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 = 0.3659 r_free = 0.3659 target = 0.149685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.120333 restraints weight = 5740.645| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.40 r_work: 0.3284 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5830 Z= 0.156 Angle : 0.543 6.550 7899 Z= 0.277 Chirality : 0.043 0.159 885 Planarity : 0.004 0.049 1005 Dihedral : 7.491 63.242 814 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 4.17 % Allowed : 22.76 % 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 aren not related in a simple way. whole: 1.60 (0.33), residues: 703 helix: 1.48 (0.27), residues: 385 sheet: -0.15 (0.53), residues: 80 loop : 1.06 (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 0.004 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5830) covalent geometry : angle 0.54269 ( 7899) hydrogen bonds : bond 0.03995 ( 318) hydrogen bonds : angle 4.62445 ( 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 118 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6652 (tm-30) REVERT: A 223 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6989 (mm-30) REVERT: A 347 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7351 (ptmt) REVERT: B 74 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6560 (pp20) REVERT: B 97 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7202 (mtp180) outliers start: 26 outliers final: 14 residues processed: 109 average time/residue: 0.6461 time to fit residues: 73.2846 Evaluate side-chains 108 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain B residue 346 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 39 optimal weight: 0.3980 chunk 66 optimal weight: 0.0980 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.0670 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 148 ASN 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 = 0.3776 r_free = 0.3776 target = 0.159253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133161 restraints weight = 5742.611| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.33 r_work: 0.3347 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5830 Z= 0.106 Angle : 0.504 6.443 7899 Z= 0.255 Chirality : 0.041 0.148 885 Planarity : 0.004 0.048 1005 Dihedral : 7.070 60.606 814 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.21 % Allowed : 23.72 % 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 aren not related in a simple way. whole: 1.79 (0.33), residues: 703 helix: 1.69 (0.27), residues: 381 sheet: 0.09 (0.54), residues: 79 loop : 0.97 (0.45), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 185 TYR 0.012 0.001 TYR A 42 PHE 0.011 0.001 PHE A 125 TRP 0.011 0.002 TRP A 277 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 5830) covalent geometry : angle 0.50398 ( 7899) hydrogen bonds : bond 0.03504 ( 318) hydrogen bonds : angle 4.41012 ( 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 115 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6970 (mm-30) REVERT: A 346 GLN cc_start: 0.7499 (tp40) cc_final: 0.7120 (mm110) REVERT: B 74 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6608 (pp20) REVERT: B 97 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7156 (mtt180) outliers start: 20 outliers final: 9 residues processed: 107 average time/residue: 0.5711 time to fit residues: 63.7124 Evaluate side-chains 107 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 265 ASN Chi-restraints excluded: chain A residue 321 ASP 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 205 THR Chi-restraints excluded: chain B residue 288 ASP 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: 0.8980 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.153360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.125328 restraints weight = 5811.078| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.33 r_work: 0.3296 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1210 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= 0.165 Angle : 0.556 6.337 7899 Z= 0.284 Chirality : 0.044 0.164 885 Planarity : 0.004 0.050 1005 Dihedral : 7.428 65.253 814 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.40 % Allowed : 25.32 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.33), residues: 703 helix: 1.50 (0.27), residues: 386 sheet: 0.04 (0.56), residues: 73 loop : 0.98 (0.45), residues: 244 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 0.015 0.001 PHE A 125 TRP 0.008 0.002 TRP A 277 HIS 0.005 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 5830) covalent geometry : angle 0.55580 ( 7899) hydrogen bonds : bond 0.03982 ( 318) hydrogen bonds : angle 4.58107 ( 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 108 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7010 (mm-30) REVERT: B 74 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6552 (pp20) REVERT: B 97 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7143 (mtp180) outliers start: 15 outliers final: 9 residues processed: 102 average time/residue: 0.5740 time to fit residues: 61.1638 Evaluate side-chains 102 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 265 ASN Chi-restraints excluded: chain A residue 321 ASP 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 205 THR Chi-restraints excluded: chain B residue 288 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 63 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3720 r_free = 0.3720 target = 0.154455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.126620 restraints weight = 5722.107| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.33 r_work: 0.3291 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1242 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= 0.137 Angle : 0.536 6.353 7899 Z= 0.272 Chirality : 0.043 0.158 885 Planarity : 0.004 0.049 1005 Dihedral : 7.482 64.348 814 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.08 % Allowed : 25.64 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.33), residues: 703 helix: 1.52 (0.27), residues: 387 sheet: 0.05 (0.56), residues: 73 loop : 0.96 (0.45), residues: 243 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 0.014 0.001 PHE A 125 TRP 0.009 0.001 TRP A 277 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5830) covalent geometry : angle 0.53615 ( 7899) hydrogen bonds : bond 0.03794 ( 318) hydrogen bonds : angle 4.53508 ( 882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2308.43 seconds wall clock time: 40 minutes 5.84 seconds (2405.84 seconds total)