Starting phenix.real_space_refine on Thu Mar 6 09:32:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jo4_36455/03_2025/8jo4_36455_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jo4_36455/03_2025/8jo4_36455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jo4_36455/03_2025/8jo4_36455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jo4_36455/03_2025/8jo4_36455.map" model { file = "/net/cci-nas-00/data/ceres_data/8jo4_36455/03_2025/8jo4_36455_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jo4_36455/03_2025/8jo4_36455_neut.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.001 sd= 0.078 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 6 5.49 5 Mg 1 5.21 5 S 27 5.16 5 C 3616 2.51 5 N 951 2.21 5 O 1117 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5719 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2846 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 4.07, per 1000 atoms: 0.71 Number of scatterers: 5719 At special positions: 0 Unit cell: (64.17, 80.91, 113.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 27 16.00 P 6 15.00 Mg 1 11.99 O 1117 8.00 N 951 7.00 C 3616 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: 1.41 Conformation dependent library (CDL) restraints added in 831.7 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 59.8% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 41 through 55 removed outlier: 3.659A 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 89 removed outlier: 3.693A pdb=" N SER A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 118 Processing helix chain 'A' and resid 121 through 134 removed outlier: 4.226A 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 259 removed outlier: 3.795A 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: 3.552A pdb=" N VAL A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 removed outlier: 3.660A 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 93 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: 3.782A 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 218 Processing helix chain 'B' and resid 224 through 235 Processing helix chain 'B' and resid 254 through 262 removed outlier: 3.548A pdb=" N CYS B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) 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 291 through 298 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: 3.908A 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: 3.728A 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: 6.180A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 8.108A 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: 6.274A 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 243 317 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.69 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: 1854 1.34 - 1.46: 1040 1.46 - 1.57: 2881 1.57 - 1.69: 10 1.69 - 1.81: 47 Bond restraints: 5832 Sorted by residual: bond pdb=" N ILE A 316 " pdb=" CA ILE A 316 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.17e-02 7.31e+03 1.03e+01 bond pdb=" N ILE B 359 " pdb=" CA ILE B 359 " ideal model delta sigma weight residual 1.461 1.490 -0.030 1.08e-02 8.57e+03 7.65e+00 bond pdb=" N ASN A 164 " pdb=" CA ASN A 164 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.27e-02 6.20e+03 7.00e+00 bond pdb=" N SER A 22 " pdb=" CA SER A 22 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 4.92e+00 bond pdb=" N ARG A 185 " pdb=" CA ARG A 185 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.33e-02 5.65e+03 4.87e+00 ... (remaining 5827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 7744 1.67 - 3.33: 128 3.33 - 5.00: 28 5.00 - 6.67: 2 6.67 - 8.34: 3 Bond angle restraints: 7905 Sorted by residual: angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 131.70 8.17 1.00e+00 1.00e+00 6.67e+01 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 132.54 4.29 1.00e+00 1.00e+00 1.84e+01 angle pdb=" C SER B 273 " pdb=" CA SER B 273 " pdb=" CB SER B 273 " ideal model delta sigma weight residual 111.78 103.44 8.34 2.20e+00 2.07e-01 1.44e+01 angle pdb=" N THR B 360 " pdb=" CA THR B 360 " pdb=" C THR B 360 " ideal model delta sigma weight residual 110.55 105.47 5.08 1.35e+00 5.49e-01 1.41e+01 angle pdb=" N ILE B 359 " pdb=" CA ILE B 359 " pdb=" C ILE B 359 " ideal model delta sigma weight residual 108.12 103.61 4.51 1.34e+00 5.57e-01 1.13e+01 ... (remaining 7900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 3312 17.66 - 35.32: 198 35.32 - 52.98: 61 52.98 - 70.64: 16 70.64 - 88.30: 4 Dihedral angle restraints: 3591 sinusoidal: 1502 harmonic: 2089 Sorted by residual: dihedral pdb=" C SER B 273 " pdb=" N SER B 273 " pdb=" CA SER B 273 " pdb=" CB SER B 273 " ideal model delta harmonic sigma weight residual -122.60 -113.53 -9.07 0 2.50e+00 1.60e-01 1.32e+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 180.00 163.26 16.74 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA HIS B 163 " pdb=" C HIS B 163 " pdb=" N ASN B 164 " pdb=" CA ASN B 164 " ideal model delta harmonic sigma weight residual 180.00 163.36 16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 3588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 739 0.056 - 0.112: 126 0.112 - 0.168: 15 0.168 - 0.224: 3 0.224 - 0.280: 2 Chirality restraints: 885 Sorted by residual: chirality pdb=" CA ILE B 359 " pdb=" N ILE B 359 " pdb=" C ILE B 359 " pdb=" CB ILE B 359 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA MET A 162 " pdb=" N MET A 162 " pdb=" C MET A 162 " pdb=" CB MET A 162 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA SER B 273 " pdb=" N SER B 273 " pdb=" C SER B 273 " pdb=" CB SER B 273 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 882 not shown) Planarity restraints: 1004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 211 " -0.044 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO A 212 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 165 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B 166 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 161 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C VAL A 161 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL A 161 " 0.008 2.00e-02 2.50e+03 pdb=" N MET A 162 " 0.007 2.00e-02 2.50e+03 ... (remaining 1001 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 589 2.74 - 3.28: 5909 3.28 - 3.82: 10157 3.82 - 4.36: 12580 4.36 - 4.90: 21365 Nonbonded interactions: 50600 Sorted by model distance: nonbonded pdb=" NE2 HIS B 90 " pdb=" OE2 GLU B 95 " model vdw 2.202 3.120 nonbonded pdb=" OE2 GLU A 343 " pdb=" OG SER B 352 " model vdw 2.216 3.040 nonbonded pdb=" OG SER A 175 " pdb=" OD2 ASP A 298 " model vdw 2.228 3.040 nonbonded pdb=" O GLY B 158 " pdb=" OG1 THR B 305 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASP A 23 " pdb=" OG SER A 100 " model vdw 2.243 3.040 ... (remaining 50595 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.680 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 : 0.004 0.040 5832 Z= 0.281 Angle : 0.588 8.337 7905 Z= 0.350 Chirality : 0.046 0.280 885 Planarity : 0.004 0.067 1004 Dihedral : 13.286 88.300 2243 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.99 % Favored : 97.87 % Rotamer: Outliers : 3.21 % Allowed : 4.01 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.32), residues: 703 helix: 1.15 (0.27), residues: 377 sheet: -0.26 (0.58), residues: 71 loop : 0.54 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 277 HIS 0.005 0.001 HIS A 300 PHE 0.012 0.001 PHE A 125 TYR 0.011 0.001 TYR A 42 ARG 0.002 0.000 ARG B 198 *********************** 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 149 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7429 (tt) REVERT: A 129 ASN cc_start: 0.6919 (t0) cc_final: 0.6595 (t0) REVERT: A 162 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6515 (mtp) REVERT: B 35 SER cc_start: 0.8187 (p) cc_final: 0.7903 (t) REVERT: B 298 ASN cc_start: 0.7642 (m-40) cc_final: 0.7382 (m-40) REVERT: B 336 GLU cc_start: 0.6742 (pm20) cc_final: 0.6372 (pm20) outliers start: 20 outliers final: 7 residues processed: 142 average time/residue: 0.1837 time to fit residues: 33.4825 Evaluate side-chains 97 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 346 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 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 142 ASN B 299 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 = 0.3857 r_free = 0.3857 target = 0.154579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.131983 restraints weight = 6337.225| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.64 r_work: 0.3484 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5832 Z= 0.220 Angle : 0.507 4.804 7905 Z= 0.270 Chirality : 0.043 0.155 885 Planarity : 0.004 0.062 1004 Dihedral : 10.217 86.017 856 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.28 % Favored : 98.58 % Rotamer: Outliers : 3.05 % Allowed : 10.11 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.32), residues: 703 helix: 1.31 (0.26), residues: 382 sheet: 0.46 (0.58), residues: 71 loop : 0.55 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 277 HIS 0.006 0.001 HIS B 75 PHE 0.013 0.001 PHE A 125 TYR 0.035 0.001 TYR A 52 ARG 0.004 0.000 ARG A 307 *********************** 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 116 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7306 (tt) REVERT: A 129 ASN cc_start: 0.7136 (t0) cc_final: 0.6724 (t0) REVERT: B 95 GLU cc_start: 0.6586 (tp30) cc_final: 0.5587 (tp30) REVERT: B 298 ASN cc_start: 0.7443 (m-40) cc_final: 0.7190 (m-40) REVERT: B 336 GLU cc_start: 0.6825 (pm20) cc_final: 0.6513 (pm20) outliers start: 19 outliers final: 9 residues processed: 110 average time/residue: 0.1879 time to fit residues: 26.8676 Evaluate side-chains 91 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 331 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 75 HIS B 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.153092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129319 restraints weight = 6505.696| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.81 r_work: 0.3444 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5832 Z= 0.271 Angle : 0.529 6.323 7905 Z= 0.278 Chirality : 0.044 0.169 885 Planarity : 0.004 0.061 1004 Dihedral : 9.386 89.711 845 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.99 % Favored : 97.87 % Rotamer: Outliers : 2.73 % Allowed : 9.47 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.32), residues: 703 helix: 1.35 (0.26), residues: 382 sheet: 0.60 (0.60), residues: 71 loop : 0.53 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 277 HIS 0.004 0.001 HIS B 75 PHE 0.013 0.002 PHE A 125 TYR 0.045 0.002 TYR A 52 ARG 0.005 0.001 ARG A 154 *********************** 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 108 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7324 (tt) REVERT: A 129 ASN cc_start: 0.7060 (t0) cc_final: 0.6680 (t0) REVERT: A 186 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6504 (mt-10) REVERT: B 95 GLU cc_start: 0.6672 (tp30) cc_final: 0.5622 (tp30) REVERT: B 134 MET cc_start: 0.7714 (ttp) cc_final: 0.7252 (ttp) REVERT: B 298 ASN cc_start: 0.7514 (m-40) cc_final: 0.7187 (m-40) REVERT: B 315 MET cc_start: 0.7206 (tpp) cc_final: 0.7002 (tpp) REVERT: B 336 GLU cc_start: 0.6939 (pm20) cc_final: 0.6652 (pm20) outliers start: 17 outliers final: 10 residues processed: 102 average time/residue: 0.1736 time to fit residues: 23.5990 Evaluate side-chains 95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 300 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 68 optimal weight: 0.0050 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.156274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132705 restraints weight = 6554.259| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.82 r_work: 0.3474 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5832 Z= 0.178 Angle : 0.472 4.744 7905 Z= 0.252 Chirality : 0.042 0.132 885 Planarity : 0.004 0.059 1004 Dihedral : 9.003 84.822 845 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.71 % Favored : 98.15 % Rotamer: Outliers : 2.25 % Allowed : 11.88 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.32), residues: 703 helix: 1.60 (0.26), residues: 383 sheet: 0.72 (0.60), residues: 71 loop : 0.70 (0.42), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 358 HIS 0.002 0.001 HIS A 300 PHE 0.015 0.001 PHE B 257 TYR 0.052 0.001 TYR A 52 ARG 0.005 0.000 ARG A 154 *********************** 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 108 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 129 ASN cc_start: 0.7149 (t0) cc_final: 0.6753 (t0) REVERT: A 134 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7490 (mt-10) REVERT: A 307 ARG cc_start: 0.8122 (mtm110) cc_final: 0.7822 (mtp180) REVERT: B 95 GLU cc_start: 0.6612 (tp30) cc_final: 0.5598 (tp30) REVERT: B 243 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6745 (mm-30) REVERT: B 298 ASN cc_start: 0.7458 (m-40) cc_final: 0.7144 (m-40) REVERT: B 336 GLU cc_start: 0.7000 (pm20) cc_final: 0.6650 (pm20) outliers start: 14 outliers final: 8 residues processed: 104 average time/residue: 0.1985 time to fit residues: 26.6521 Evaluate side-chains 90 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.156514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133341 restraints weight = 6411.222| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.75 r_work: 0.3484 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5832 Z= 0.188 Angle : 0.479 8.353 7905 Z= 0.254 Chirality : 0.042 0.128 885 Planarity : 0.004 0.059 1004 Dihedral : 8.475 82.983 841 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.85 % Favored : 98.01 % Rotamer: Outliers : 2.57 % Allowed : 12.68 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.32), residues: 703 helix: 1.64 (0.26), residues: 382 sheet: 0.93 (0.61), residues: 71 loop : 0.79 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 277 HIS 0.003 0.001 HIS A 300 PHE 0.015 0.001 PHE B 257 TYR 0.037 0.001 TYR A 52 ARG 0.005 0.000 ARG A 154 *********************** 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 104 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7482 (tp30) cc_final: 0.6876 (mt-10) REVERT: A 129 ASN cc_start: 0.7145 (t0) cc_final: 0.6745 (t0) REVERT: A 134 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7484 (mt-10) REVERT: A 186 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6536 (mt-10) REVERT: A 295 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.6979 (mp) REVERT: A 340 MET cc_start: 0.8084 (tmm) cc_final: 0.7871 (ttp) REVERT: B 95 GLU cc_start: 0.6592 (tp30) cc_final: 0.5605 (tp30) REVERT: B 243 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6687 (mm-30) REVERT: B 336 GLU cc_start: 0.7041 (pm20) cc_final: 0.6705 (pm20) outliers start: 16 outliers final: 11 residues processed: 100 average time/residue: 0.1779 time to fit residues: 23.6765 Evaluate side-chains 98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.156397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.132728 restraints weight = 6426.263| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.81 r_work: 0.3476 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5832 Z= 0.208 Angle : 0.488 7.866 7905 Z= 0.258 Chirality : 0.042 0.128 885 Planarity : 0.004 0.060 1004 Dihedral : 8.381 82.124 841 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.71 % Favored : 98.15 % Rotamer: Outliers : 2.25 % Allowed : 13.16 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.32), residues: 703 helix: 1.63 (0.26), residues: 382 sheet: 1.07 (0.63), residues: 69 loop : 0.76 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 277 HIS 0.003 0.001 HIS A 300 PHE 0.022 0.002 PHE A 24 TYR 0.024 0.001 TYR A 52 ARG 0.005 0.000 ARG A 154 *********************** 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 99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7335 (tp30) cc_final: 0.6792 (mt-10) REVERT: A 52 TYR cc_start: 0.7419 (m-80) cc_final: 0.7140 (m-80) REVERT: A 129 ASN cc_start: 0.7156 (t0) cc_final: 0.6758 (t0) REVERT: A 134 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7455 (mt-10) REVERT: A 186 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6566 (mt-10) REVERT: A 295 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7013 (mp) REVERT: A 307 ARG cc_start: 0.8273 (ptp-110) cc_final: 0.7883 (mtp180) REVERT: A 340 MET cc_start: 0.8094 (tmm) cc_final: 0.7816 (ttp) REVERT: B 243 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6693 (mm-30) REVERT: B 336 GLU cc_start: 0.7087 (pm20) cc_final: 0.6730 (pm20) outliers start: 14 outliers final: 9 residues processed: 95 average time/residue: 0.1856 time to fit residues: 23.1731 Evaluate side-chains 94 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130917 restraints weight = 6492.639| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.82 r_work: 0.3454 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5832 Z= 0.250 Angle : 0.507 6.811 7905 Z= 0.270 Chirality : 0.043 0.136 885 Planarity : 0.004 0.060 1004 Dihedral : 8.431 82.954 841 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.57 % Allowed : 12.84 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.32), residues: 703 helix: 1.56 (0.26), residues: 382 sheet: 1.06 (0.64), residues: 69 loop : 0.72 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 277 HIS 0.003 0.001 HIS A 300 PHE 0.022 0.002 PHE A 31 TYR 0.014 0.001 TYR A 42 ARG 0.004 0.000 ARG A 154 *********************** 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 100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7483 (tp30) cc_final: 0.6896 (mt-10) REVERT: A 52 TYR cc_start: 0.7428 (m-80) cc_final: 0.7172 (m-80) REVERT: A 129 ASN cc_start: 0.7031 (t0) cc_final: 0.6640 (t0) REVERT: A 186 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6556 (mt-10) REVERT: A 295 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7007 (mp) REVERT: A 307 ARG cc_start: 0.8265 (ptp-110) cc_final: 0.7893 (mtp180) REVERT: A 340 MET cc_start: 0.8150 (tmm) cc_final: 0.7868 (ttp) REVERT: B 95 GLU cc_start: 0.6678 (tp30) cc_final: 0.6072 (mm-30) REVERT: B 243 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6740 (mm-30) REVERT: B 336 GLU cc_start: 0.7082 (pm20) cc_final: 0.6732 (pm20) REVERT: B 377 PHE cc_start: 0.8010 (p90) cc_final: 0.7724 (p90) outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 0.2096 time to fit residues: 26.4374 Evaluate side-chains 97 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.157531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.134288 restraints weight = 6379.804| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.79 r_work: 0.3485 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5832 Z= 0.180 Angle : 0.472 5.976 7905 Z= 0.252 Chirality : 0.041 0.126 885 Planarity : 0.004 0.059 1004 Dihedral : 8.216 80.794 841 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.73 % Allowed : 12.20 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.32), residues: 703 helix: 1.68 (0.26), residues: 382 sheet: 1.17 (0.65), residues: 69 loop : 0.78 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.003 0.001 HIS A 300 PHE 0.018 0.002 PHE A 24 TYR 0.012 0.001 TYR A 42 ARG 0.007 0.000 ARG A 154 *********************** 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 110 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.702 Fit side-chains REVERT: A 33 GLU cc_start: 0.7417 (tp30) cc_final: 0.6824 (mt-10) REVERT: A 52 TYR cc_start: 0.7382 (m-80) cc_final: 0.6892 (m-10) REVERT: A 129 ASN cc_start: 0.7143 (t0) cc_final: 0.6740 (t0) REVERT: A 186 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6612 (mt-10) REVERT: A 295 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7007 (mp) REVERT: B 95 GLU cc_start: 0.6633 (tp30) cc_final: 0.6201 (mm-30) REVERT: B 108 THR cc_start: 0.7448 (p) cc_final: 0.7187 (p) REVERT: B 243 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6754 (mm-30) REVERT: B 336 GLU cc_start: 0.7049 (pm20) cc_final: 0.6694 (pm20) REVERT: B 377 PHE cc_start: 0.7915 (p90) cc_final: 0.7638 (p90) outliers start: 17 outliers final: 12 residues processed: 106 average time/residue: 0.1829 time to fit residues: 25.7378 Evaluate side-chains 98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 313 ASP 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 51 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.154789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.131719 restraints weight = 6557.991| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.76 r_work: 0.3468 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5832 Z= 0.239 Angle : 0.505 6.181 7905 Z= 0.268 Chirality : 0.043 0.128 885 Planarity : 0.004 0.060 1004 Dihedral : 8.274 82.355 841 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.73 % Allowed : 13.48 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.32), residues: 703 helix: 1.56 (0.26), residues: 382 sheet: 1.08 (0.64), residues: 69 loop : 0.78 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 277 HIS 0.003 0.001 HIS A 300 PHE 0.026 0.002 PHE A 24 TYR 0.014 0.001 TYR A 42 ARG 0.007 0.000 ARG A 154 *********************** 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 105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 1.362 Fit side-chains REVERT: A 33 GLU cc_start: 0.7456 (tp30) cc_final: 0.6758 (mt-10) REVERT: A 52 TYR cc_start: 0.7439 (m-80) cc_final: 0.6961 (m-10) REVERT: A 129 ASN cc_start: 0.7083 (t0) cc_final: 0.6687 (t0) REVERT: A 134 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7406 (mt-10) REVERT: A 186 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6672 (mt-10) REVERT: A 295 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7031 (mp) REVERT: B 95 GLU cc_start: 0.6657 (tp30) cc_final: 0.6124 (mm-30) REVERT: B 243 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6675 (mm-30) REVERT: B 336 GLU cc_start: 0.7089 (pm20) cc_final: 0.6757 (pm20) REVERT: B 377 PHE cc_start: 0.7891 (p90) cc_final: 0.7634 (p90) outliers start: 17 outliers final: 13 residues processed: 100 average time/residue: 0.2468 time to fit residues: 33.3279 Evaluate side-chains 101 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 346 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.153797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.130211 restraints weight = 6586.667| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 1.82 r_work: 0.3445 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5832 Z= 0.262 Angle : 0.521 6.179 7905 Z= 0.276 Chirality : 0.043 0.129 885 Planarity : 0.004 0.060 1004 Dihedral : 8.369 84.248 841 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.73 % Allowed : 13.80 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.32), residues: 703 helix: 1.48 (0.26), residues: 382 sheet: 1.01 (0.63), residues: 69 loop : 0.74 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 277 HIS 0.003 0.001 HIS A 300 PHE 0.026 0.002 PHE A 24 TYR 0.014 0.001 TYR A 42 ARG 0.007 0.000 ARG A 154 ********************** 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 102 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.680 Fit side-chains REVERT: A 33 GLU cc_start: 0.7447 (tp30) cc_final: 0.6912 (mt-10) REVERT: A 52 TYR cc_start: 0.7508 (m-80) cc_final: 0.7045 (m-10) REVERT: A 129 ASN cc_start: 0.6930 (t0) cc_final: 0.6533 (t0) REVERT: A 186 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6660 (mt-10) REVERT: A 295 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7031 (mp) REVERT: A 307 ARG cc_start: 0.8226 (ptp-110) cc_final: 0.7838 (mtp180) REVERT: B 95 GLU cc_start: 0.6726 (tp30) cc_final: 0.6476 (mm-30) REVERT: B 243 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6698 (mm-30) REVERT: B 336 GLU cc_start: 0.7102 (pm20) cc_final: 0.6753 (pm20) REVERT: B 377 PHE cc_start: 0.7900 (p90) cc_final: 0.7594 (p90) outliers start: 17 outliers final: 13 residues processed: 98 average time/residue: 0.1948 time to fit residues: 25.2281 Evaluate side-chains 100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 346 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.155217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132613 restraints weight = 6569.994| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.71 r_work: 0.3479 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5832 Z= 0.212 Angle : 0.498 5.383 7905 Z= 0.264 Chirality : 0.043 0.127 885 Planarity : 0.004 0.059 1004 Dihedral : 8.245 83.133 841 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.41 % Allowed : 14.45 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.32), residues: 703 helix: 1.55 (0.26), residues: 382 sheet: 1.03 (0.64), residues: 69 loop : 0.80 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 358 HIS 0.003 0.001 HIS A 300 PHE 0.034 0.002 PHE A 31 TYR 0.013 0.001 TYR A 42 ARG 0.006 0.000 ARG A 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3416.68 seconds wall clock time: 60 minutes 37.19 seconds (3637.19 seconds total)