Starting phenix.real_space_refine on Thu Nov 14 10:21:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo4_36455/11_2024/8jo4_36455_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo4_36455/11_2024/8jo4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo4_36455/11_2024/8jo4_36455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo4_36455/11_2024/8jo4_36455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo4_36455/11_2024/8jo4_36455_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jo4_36455/11_2024/8jo4_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-5513/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: 4.21, per 1000 atoms: 0.74 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: 1.58 Conformation dependent library (CDL) restraints added in 866.4 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: 0.69 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: 1.63 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 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: 0.670 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.770 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.850 ------------------------------------------------------------------------------- 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 : 0.655 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: 0.2054 time to fit residues: 37.4127 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 : 0.627 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1468 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= 0.221 Angle : 0.507 4.809 7905 Z= 0.270 Chirality : 0.043 0.156 885 Planarity : 0.004 0.062 1004 Dihedral : 10.224 85.961 856 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.35 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: 1.29 (0.26), residues: 382 sheet: 0.46 (0.58), residues: 71 loop : 0.59 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 : 0.718 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7339 (tt) REVERT: A 129 ASN cc_start: 0.7024 (t0) cc_final: 0.6632 (t0) REVERT: B 95 GLU cc_start: 0.6447 (tp30) cc_final: 0.5451 (tp30) REVERT: B 298 ASN cc_start: 0.7478 (m-40) cc_final: 0.7274 (m-40) REVERT: B 336 GLU cc_start: 0.6556 (pm20) cc_final: 0.6306 (pm20) outliers start: 19 outliers final: 9 residues processed: 110 average time/residue: 0.1945 time to fit residues: 28.1171 Evaluate side-chains 92 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 35 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1826 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= 0.195 Angle : 0.491 5.401 7905 Z= 0.258 Chirality : 0.042 0.174 885 Planarity : 0.004 0.060 1004 Dihedral : 9.166 84.767 845 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.71 % Favored : 98.15 % Rotamer: Outliers : 2.41 % Allowed : 9.79 % 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: 1.60 (0.32), residues: 703 helix: 1.51 (0.26), residues: 383 sheet: 0.74 (0.61), residues: 71 loop : 0.65 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 277 HIS 0.004 0.001 HIS B 75 PHE 0.014 0.001 PHE B 257 TYR 0.047 0.001 TYR A 52 ARG 0.005 0.001 ARG B 212 *********************** 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 107 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 129 ASN cc_start: 0.7036 (t0) cc_final: 0.6648 (t0) REVERT: A 186 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6432 (mt-10) REVERT: A 340 MET cc_start: 0.8130 (tmm) cc_final: 0.7879 (ttp) REVERT: B 95 GLU cc_start: 0.6399 (tp30) cc_final: 0.5440 (tp30) REVERT: B 134 MET cc_start: 0.7632 (ttp) cc_final: 0.7211 (ttp) REVERT: B 243 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6494 (mm-30) REVERT: B 298 ASN cc_start: 0.7404 (m-40) cc_final: 0.7140 (m-40) REVERT: B 315 MET cc_start: 0.7531 (tpp) cc_final: 0.7215 (mmt) REVERT: B 336 GLU cc_start: 0.6616 (pm20) cc_final: 0.6332 (pm20) outliers start: 15 outliers final: 6 residues processed: 102 average time/residue: 0.1801 time to fit residues: 24.4905 Evaluate side-chains 85 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 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 243 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 0.0870 chunk 30 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5832 Z= 0.157 Angle : 0.465 7.955 7905 Z= 0.246 Chirality : 0.041 0.125 885 Planarity : 0.004 0.059 1004 Dihedral : 8.462 81.024 841 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.56 % Favored : 98.29 % Rotamer: Outliers : 1.77 % Allowed : 12.04 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.87 (0.32), residues: 703 helix: 1.73 (0.26), residues: 383 sheet: 0.86 (0.60), residues: 71 loop : 0.76 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 277 HIS 0.002 0.001 HIS A 300 PHE 0.014 0.001 PHE A 24 TYR 0.040 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: 11 poor density : 97 time to evaluate : 0.648 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7542 (tp30) cc_final: 0.7068 (mt-10) REVERT: A 129 ASN cc_start: 0.6992 (t0) cc_final: 0.6614 (t0) REVERT: A 295 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.6982 (mp) REVERT: A 340 MET cc_start: 0.8047 (tmm) cc_final: 0.7826 (ttp) REVERT: B 95 GLU cc_start: 0.6309 (tp30) cc_final: 0.5426 (tp30) REVERT: B 108 THR cc_start: 0.7726 (p) cc_final: 0.7452 (p) REVERT: B 121 MET cc_start: 0.7513 (ttm) cc_final: 0.7183 (ttp) REVERT: B 336 GLU cc_start: 0.6678 (pm20) cc_final: 0.6409 (pm20) outliers start: 11 outliers final: 5 residues processed: 104 average time/residue: 0.2010 time to fit residues: 26.8623 Evaluate side-chains 87 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5832 Z= 0.298 Angle : 0.531 8.373 7905 Z= 0.279 Chirality : 0.044 0.130 885 Planarity : 0.004 0.061 1004 Dihedral : 8.699 86.513 841 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.99 % Favored : 97.87 % Rotamer: Outliers : 2.57 % Allowed : 12.52 % Favored : 84.91 % 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: 1.59 (0.32), residues: 703 helix: 1.48 (0.26), residues: 382 sheet: 0.74 (0.59), residues: 71 loop : 0.68 (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 A 300 PHE 0.018 0.002 PHE A 24 TYR 0.036 0.002 TYR A 52 ARG 0.006 0.001 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 : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7584 (tp30) cc_final: 0.7071 (mt-10) REVERT: A 129 ASN cc_start: 0.6913 (t0) cc_final: 0.6559 (t0) REVERT: A 186 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6604 (mt-10) REVERT: B 134 MET cc_start: 0.7556 (ttp) cc_final: 0.7160 (ttt) REVERT: B 243 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6504 (mm-30) REVERT: B 298 ASN cc_start: 0.7791 (m-40) cc_final: 0.7566 (m-40) REVERT: B 336 GLU cc_start: 0.6737 (pm20) cc_final: 0.6481 (pm20) outliers start: 16 outliers final: 11 residues processed: 100 average time/residue: 0.1837 time to fit residues: 24.3096 Evaluate side-chains 97 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 184 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 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 16 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5832 Z= 0.199 Angle : 0.486 6.501 7905 Z= 0.258 Chirality : 0.042 0.129 885 Planarity : 0.004 0.060 1004 Dihedral : 8.462 82.310 841 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.56 % Favored : 98.29 % Rotamer: Outliers : 2.41 % Allowed : 13.00 % 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: 1.76 (0.32), residues: 703 helix: 1.58 (0.26), residues: 382 sheet: 0.91 (0.60), residues: 71 loop : 0.79 (0.42), residues: 250 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 0.018 0.002 PHE A 24 TYR 0.036 0.001 TYR A 52 ARG 0.005 0.000 ARG A 117 *********************** 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 105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7611 (tp30) cc_final: 0.7078 (mt-10) REVERT: A 129 ASN cc_start: 0.6918 (t0) cc_final: 0.6531 (t0) REVERT: A 186 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6633 (mt-10) REVERT: A 340 MET cc_start: 0.8052 (tmm) cc_final: 0.7812 (ttp) REVERT: B 134 MET cc_start: 0.7366 (ttp) cc_final: 0.6977 (ttt) REVERT: B 243 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6568 (mm-30) REVERT: B 336 GLU cc_start: 0.6735 (pm20) cc_final: 0.6476 (pm20) outliers start: 15 outliers final: 11 residues processed: 100 average time/residue: 0.1721 time to fit residues: 22.9938 Evaluate side-chains 95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 184 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 209 GLU 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 38 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5832 Z= 0.236 Angle : 0.508 6.367 7905 Z= 0.270 Chirality : 0.043 0.129 885 Planarity : 0.004 0.060 1004 Dihedral : 8.426 82.601 841 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.57 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: 1.71 (0.32), residues: 703 helix: 1.56 (0.26), residues: 382 sheet: 0.99 (0.63), 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 0.017 0.002 PHE A 24 TYR 0.022 0.001 TYR A 52 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 99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7602 (tp30) cc_final: 0.7063 (mt-10) REVERT: A 129 ASN cc_start: 0.6894 (t0) cc_final: 0.6515 (t0) REVERT: A 186 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6655 (mt-10) REVERT: A 295 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7093 (mp) REVERT: A 340 MET cc_start: 0.8106 (tmm) cc_final: 0.7843 (ttp) REVERT: B 134 MET cc_start: 0.7419 (ttp) cc_final: 0.7007 (ttt) REVERT: B 243 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6455 (mm-30) REVERT: B 336 GLU cc_start: 0.6712 (pm20) cc_final: 0.6450 (pm20) outliers start: 16 outliers final: 12 residues processed: 95 average time/residue: 0.1932 time to fit residues: 24.3356 Evaluate side-chains 96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 184 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 13 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 58 optimal weight: 0.1980 chunk 62 optimal weight: 0.0060 chunk 37 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5832 Z= 0.180 Angle : 0.479 5.917 7905 Z= 0.257 Chirality : 0.041 0.126 885 Planarity : 0.004 0.060 1004 Dihedral : 8.178 80.210 841 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.25 % Allowed : 13.48 % Favored : 84.27 % 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: 1.88 (0.32), residues: 703 helix: 1.69 (0.26), residues: 382 sheet: 1.09 (0.64), residues: 69 loop : 0.80 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.003 0.001 HIS A 300 PHE 0.031 0.002 PHE A 31 TYR 0.023 0.001 TYR A 52 ARG 0.006 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 108 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7604 (tp30) cc_final: 0.7056 (mt-10) REVERT: A 52 TYR cc_start: 0.7383 (m-80) cc_final: 0.7174 (m-80) REVERT: A 129 ASN cc_start: 0.6908 (t0) cc_final: 0.6530 (t0) REVERT: A 186 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6675 (mt-10) REVERT: A 295 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7065 (mp) REVERT: B 108 THR cc_start: 0.7731 (p) cc_final: 0.7358 (p) REVERT: B 243 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6499 (mm-30) REVERT: B 336 GLU cc_start: 0.6702 (pm20) cc_final: 0.6434 (pm20) outliers start: 14 outliers final: 10 residues processed: 102 average time/residue: 0.1791 time to fit residues: 24.2261 Evaluate side-chains 98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 0.0040 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5832 Z= 0.177 Angle : 0.480 5.667 7905 Z= 0.256 Chirality : 0.042 0.127 885 Planarity : 0.004 0.060 1004 Dihedral : 8.069 80.223 841 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.09 % Allowed : 14.61 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.92 (0.32), residues: 703 helix: 1.69 (0.26), residues: 382 sheet: 1.14 (0.64), residues: 69 loop : 0.83 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 277 HIS 0.003 0.001 HIS A 300 PHE 0.028 0.002 PHE A 31 TYR 0.017 0.001 TYR A 52 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 98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7603 (tp30) cc_final: 0.7061 (mt-10) REVERT: A 129 ASN cc_start: 0.6962 (t0) cc_final: 0.6602 (t0) REVERT: A 186 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6215 (mp0) REVERT: A 295 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7061 (mp) REVERT: B 108 THR cc_start: 0.7748 (p) cc_final: 0.7390 (p) REVERT: B 243 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6448 (mm-30) REVERT: B 336 GLU cc_start: 0.6612 (pm20) cc_final: 0.6348 (pm20) outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 0.1602 time to fit residues: 20.3677 Evaluate side-chains 98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU 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 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 69 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.0470 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5832 Z= 0.201 Angle : 0.495 6.016 7905 Z= 0.265 Chirality : 0.042 0.140 885 Planarity : 0.004 0.060 1004 Dihedral : 8.077 81.572 841 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.93 % Allowed : 14.61 % 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: 1.83 (0.32), residues: 703 helix: 1.63 (0.26), residues: 382 sheet: 1.08 (0.64), residues: 69 loop : 0.80 (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 31 TYR 0.013 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 99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7637 (tp30) cc_final: 0.7093 (mt-10) REVERT: A 129 ASN cc_start: 0.6998 (t0) cc_final: 0.6614 (t0) REVERT: A 186 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6226 (mp0) REVERT: A 295 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7077 (mp) REVERT: B 95 GLU cc_start: 0.7034 (mm-30) cc_final: 0.5973 (mm-30) REVERT: B 108 THR cc_start: 0.7761 (p) cc_final: 0.7399 (p) REVERT: B 243 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6438 (mm-30) REVERT: B 336 GLU cc_start: 0.6687 (pm20) cc_final: 0.6421 (pm20) outliers start: 12 outliers final: 9 residues processed: 95 average time/residue: 0.1619 time to fit residues: 21.0704 Evaluate side-chains 98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 15 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.155419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.132761 restraints weight = 6421.189| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.70 r_work: 0.3479 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5832 Z= 0.213 Angle : 0.503 5.562 7905 Z= 0.269 Chirality : 0.043 0.128 885 Planarity : 0.004 0.060 1004 Dihedral : 8.043 82.657 839 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.09 % Allowed : 14.29 % Favored : 83.63 % 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: 1.77 (0.32), residues: 703 helix: 1.59 (0.26), residues: 382 sheet: 1.06 (0.64), residues: 69 loop : 0.74 (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 0.024 0.002 PHE A 31 TYR 0.014 0.001 TYR A 42 ARG 0.007 0.000 ARG A 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1631.50 seconds wall clock time: 30 minutes 31.26 seconds (1831.26 seconds total)