Starting phenix.real_space_refine on Wed Jul 1 22:28:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9utd_64489/07_2026/9utd_64489.cif Found real_map, /net/cci-nas-00/data/ceres_data/9utd_64489/07_2026/9utd_64489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9utd_64489/07_2026/9utd_64489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9utd_64489/07_2026/9utd_64489.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9utd_64489/07_2026/9utd_64489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9utd_64489/07_2026/9utd_64489.map" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 18 5.16 5 Cl 2 4.86 5 Na 1 4.78 5 C 2265 2.51 5 N 534 2.21 5 O 560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3380 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3366 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 412} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'CFA': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 0.87, per 1000 atoms: 0.26 Number of scatterers: 3380 At special positions: 0 Unit cell: (81.6, 62.9, 70.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 18 16.00 Na 1 11.00 O 560 8.00 N 534 7.00 C 2265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 467 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 91.0 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 796 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.578A pdb=" N CYS A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 57 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 66 through 75 removed outlier: 3.530A pdb=" N SER A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 111 removed outlier: 3.730A pdb=" N ILE A 80 " --> pdb=" O MET A 76 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 131 through 161 removed outlier: 3.503A pdb=" N LEU A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 169 through 182 Processing helix chain 'A' and resid 193 through 219 removed outlier: 3.542A pdb=" N SER A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A 207 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 246 removed outlier: 3.687A pdb=" N THR A 240 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.831A pdb=" N THR A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 253 " --> pdb=" O HIS A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 253' Processing helix chain 'A' and resid 266 through 275 removed outlier: 3.632A pdb=" N LEU A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU A 274 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A 275 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 292 Proline residue: A 282 - end of helix removed outlier: 3.501A pdb=" N TYR A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 308 through 323 Processing helix chain 'A' and resid 323 through 342 removed outlier: 4.126A pdb=" N GLY A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) Proline residue: A 332 - end of helix Processing helix chain 'A' and resid 348 through 356 removed outlier: 3.774A pdb=" N ARG A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 354 " --> pdb=" O CYS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 370 removed outlier: 3.621A pdb=" N ALA A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 removed outlier: 4.279A pdb=" N SER A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 390 through 401 removed outlier: 3.655A pdb=" N SER A 394 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 401 " --> pdb=" O HIS A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.534A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 438 removed outlier: 4.022A pdb=" N MET A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 459 194 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.46 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 987 1.34 - 1.46: 956 1.46 - 1.58: 1523 1.58 - 1.70: 0 1.70 - 1.82: 29 Bond restraints: 3495 Sorted by residual: bond pdb=" C1' CFA A 601 " pdb=" O1' CFA A 601 " ideal model delta sigma weight residual 1.332 1.396 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C2' CFA A 601 " pdb="CL3 CFA A 601 " ideal model delta sigma weight residual 1.727 1.783 -0.056 2.00e-02 2.50e+03 7.86e+00 bond pdb=" N LYS A 307 " pdb=" CA LYS A 307 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.26e+00 bond pdb=" N ASN A 308 " pdb=" CA ASN A 308 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.16e-02 7.43e+03 7.20e+00 bond pdb=" C4' CFA A 601 " pdb="CL4 CFA A 601 " ideal model delta sigma weight residual 1.733 1.782 -0.049 2.00e-02 2.50e+03 6.11e+00 ... (remaining 3490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 4596 1.58 - 3.15: 156 3.15 - 4.73: 16 4.73 - 6.31: 7 6.31 - 7.88: 4 Bond angle restraints: 4779 Sorted by residual: angle pdb=" N ASN A 241 " pdb=" CA ASN A 241 " pdb=" C ASN A 241 " ideal model delta sigma weight residual 111.82 107.77 4.05 1.16e+00 7.43e-01 1.22e+01 angle pdb=" CA ASN A 308 " pdb=" C ASN A 308 " pdb=" O ASN A 308 " ideal model delta sigma weight residual 121.38 118.01 3.37 1.06e+00 8.90e-01 1.01e+01 angle pdb=" O1 CFA A 601 " pdb=" C1 CFA A 601 " pdb=" O2 CFA A 601 " ideal model delta sigma weight residual 128.33 120.45 7.88 3.00e+00 1.11e-01 6.91e+00 angle pdb=" N VAL A 253 " pdb=" CA VAL A 253 " pdb=" C VAL A 253 " ideal model delta sigma weight residual 113.00 109.64 3.36 1.30e+00 5.92e-01 6.69e+00 angle pdb=" CA TYR A 69 " pdb=" CB TYR A 69 " pdb=" CG TYR A 69 " ideal model delta sigma weight residual 113.90 118.42 -4.52 1.80e+00 3.09e-01 6.32e+00 ... (remaining 4774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1736 17.96 - 35.91: 164 35.91 - 53.86: 29 53.86 - 71.82: 4 71.82 - 89.77: 3 Dihedral angle restraints: 1936 sinusoidal: 691 harmonic: 1245 Sorted by residual: dihedral pdb=" CA LEU A 357 " pdb=" C LEU A 357 " pdb=" N PRO A 358 " pdb=" CA PRO A 358 " ideal model delta harmonic sigma weight residual 180.00 149.51 30.49 0 5.00e+00 4.00e-02 3.72e+01 dihedral pdb=" CB GLU A 222 " pdb=" CG GLU A 222 " pdb=" CD GLU A 222 " pdb=" OE1 GLU A 222 " ideal model delta sinusoidal sigma weight residual 0.00 -89.77 89.77 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASN A 241 " pdb=" CB ASN A 241 " pdb=" CG ASN A 241 " pdb=" OD1 ASN A 241 " ideal model delta sinusoidal sigma weight residual 120.00 -173.20 -66.80 2 2.00e+01 2.50e-03 1.01e+01 ... (remaining 1933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 256 0.027 - 0.054: 170 0.054 - 0.081: 72 0.081 - 0.107: 25 0.107 - 0.134: 8 Chirality restraints: 531 Sorted by residual: chirality pdb=" CA PHE A 291 " pdb=" N PHE A 291 " pdb=" C PHE A 291 " pdb=" CB PHE A 291 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA HIS A 257 " pdb=" N HIS A 257 " pdb=" C HIS A 257 " pdb=" CB HIS A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA ARG A 311 " pdb=" N ARG A 311 " pdb=" C ARG A 311 " pdb=" CB ARG A 311 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 528 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO A 375 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 357 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.32e+00 pdb=" N PRO A 358 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 358 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 358 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 361 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO A 362 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " 0.021 5.00e-02 4.00e+02 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 911 2.79 - 3.32: 3003 3.32 - 3.84: 5226 3.84 - 4.37: 6317 4.37 - 4.90: 11018 Nonbonded interactions: 26475 Sorted by model distance: nonbonded pdb=" NH1 ARG A 105 " pdb=" OE2 GLU A 109 " model vdw 2.262 3.120 nonbonded pdb=" O LEU A 211 " pdb=" OG SER A 215 " model vdw 2.290 3.040 nonbonded pdb=" O GLY A 443 " pdb=" OG SER A 447 " model vdw 2.300 3.040 nonbonded pdb=" O CYS A 180 " pdb=" OG1 THR A 183 " model vdw 2.346 3.040 nonbonded pdb=" O ASN A 300 " pdb=" OG SER A 303 " model vdw 2.347 3.040 ... (remaining 26470 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.280 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: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.660 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.006 0.064 3496 Z= 0.281 Angle : 0.705 7.883 4781 Z= 0.405 Chirality : 0.042 0.134 531 Planarity : 0.006 0.081 579 Dihedral : 14.788 89.769 1137 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.94 % Allowed : 16.18 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.35), residues: 426 helix: -1.82 (0.26), residues: 306 sheet: None (None), residues: 0 loop : -3.70 (0.46), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 194 TYR 0.017 0.002 TYR A 69 PHE 0.013 0.002 PHE A 417 TRP 0.010 0.001 TRP A 134 HIS 0.007 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.28 ( 3495) covalent geometry : angle 0.70434 / 0.40 ( 4779) SS BOND : bond 0.00297 / 0.16 ( 1) SS BOND : angle 1.51701 / 0.82 ( 2) hydrogen bonds : bond 0.18738 / 13.51 ( 194) hydrogen bonds : angle 6.23814 / 4.65 ( 558) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.7925 (tpp) cc_final: 0.7634 (tpp) REVERT: A 260 TRP cc_start: 0.6972 (OUTLIER) cc_final: 0.5409 (p90) outliers start: 10 outliers final: 3 residues processed: 67 average time/residue: 0.0606 time to fit residues: 5.1428 Evaluate side-chains 46 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 TRP Chi-restraints excluded: chain A residue 319 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN A 241 ASN A 321 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.165408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123594 restraints weight = 3960.891| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.17 r_work: 0.3191 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3496 Z= 0.145 Angle : 0.569 5.758 4781 Z= 0.300 Chirality : 0.040 0.136 531 Planarity : 0.006 0.079 579 Dihedral : 6.274 63.106 467 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.82 % Allowed : 15.29 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.39), residues: 426 helix: -0.45 (0.29), residues: 303 sheet: None (None), residues: 0 loop : -3.36 (0.49), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 352 TYR 0.012 0.001 TYR A 101 PHE 0.012 0.001 PHE A 291 TRP 0.012 0.001 TRP A 134 HIS 0.002 0.001 HIS A 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 3495) covalent geometry : angle 0.56872 / 0.30 ( 4779) SS BOND : bond 0.00009 / 0.00 ( 1) SS BOND : angle 0.24821 / 0.15 ( 2) hydrogen bonds : bond 0.05272 / 3.39 ( 194) hydrogen bonds : angle 4.47306 / 3.23 ( 558) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.114 Fit side-chains REVERT: A 89 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7769 (mp) REVERT: A 103 GLU cc_start: 0.8322 (tp30) cc_final: 0.8050 (tp30) REVERT: A 127 ASP cc_start: 0.8448 (t70) cc_final: 0.8090 (t0) outliers start: 13 outliers final: 5 residues processed: 55 average time/residue: 0.0535 time to fit residues: 3.8421 Evaluate side-chains 48 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 323 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.158681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.114080 restraints weight = 3926.050| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.31 r_work: 0.3166 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3496 Z= 0.130 Angle : 0.540 8.242 4781 Z= 0.277 Chirality : 0.038 0.128 531 Planarity : 0.005 0.075 579 Dihedral : 5.215 59.600 462 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.53 % Allowed : 16.18 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.41), residues: 426 helix: 0.14 (0.30), residues: 305 sheet: None (None), residues: 0 loop : -3.25 (0.50), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 311 TYR 0.013 0.001 TYR A 244 PHE 0.012 0.001 PHE A 145 TRP 0.010 0.001 TRP A 421 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 3495) covalent geometry : angle 0.54006 / 0.28 ( 4779) SS BOND : bond 0.00107 / 0.06 ( 1) SS BOND : angle 0.23683 / 0.13 ( 2) hydrogen bonds : bond 0.05202 / 3.41 ( 194) hydrogen bonds : angle 4.17105 / 3.03 ( 558) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.121 Fit side-chains REVERT: A 89 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7067 (mp) REVERT: A 103 GLU cc_start: 0.8114 (tp30) cc_final: 0.7880 (tp30) REVERT: A 127 ASP cc_start: 0.8292 (t70) cc_final: 0.7848 (t0) REVERT: A 296 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8529 (pp) REVERT: A 453 ARG cc_start: 0.8098 (ttp-170) cc_final: 0.7709 (mtp180) outliers start: 12 outliers final: 7 residues processed: 59 average time/residue: 0.0566 time to fit residues: 4.2791 Evaluate side-chains 55 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 455 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 167 HIS A 218 HIS A 257 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.157219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113103 restraints weight = 3871.105| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.28 r_work: 0.3156 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3496 Z= 0.127 Angle : 0.523 9.550 4781 Z= 0.270 Chirality : 0.039 0.129 531 Planarity : 0.005 0.076 579 Dihedral : 5.174 59.236 462 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.53 % Allowed : 15.29 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.41), residues: 426 helix: 0.56 (0.31), residues: 297 sheet: None (None), residues: 0 loop : -2.89 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 311 TYR 0.012 0.001 TYR A 244 PHE 0.008 0.001 PHE A 246 TRP 0.008 0.001 TRP A 134 HIS 0.007 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 3495) covalent geometry : angle 0.52342 / 0.27 ( 4779) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 0.11601 / 0.06 ( 2) hydrogen bonds : bond 0.04813 / 3.15 ( 194) hydrogen bonds : angle 4.12672 / 3.01 ( 558) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.117 Fit side-chains REVERT: A 89 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7022 (mp) REVERT: A 127 ASP cc_start: 0.8371 (t70) cc_final: 0.7974 (t0) REVERT: A 181 CYS cc_start: 0.6920 (m) cc_final: 0.6410 (m) REVERT: A 296 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8478 (pp) REVERT: A 356 ARG cc_start: 0.7489 (mtm180) cc_final: 0.6818 (mtm180) outliers start: 12 outliers final: 7 residues processed: 54 average time/residue: 0.0623 time to fit residues: 4.2391 Evaluate side-chains 54 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 455 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.155138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111056 restraints weight = 3951.698| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.28 r_work: 0.3127 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3496 Z= 0.148 Angle : 0.555 9.634 4781 Z= 0.282 Chirality : 0.039 0.127 531 Planarity : 0.005 0.075 579 Dihedral : 5.082 59.426 461 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.24 % Allowed : 16.76 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.41), residues: 426 helix: 0.62 (0.31), residues: 297 sheet: None (None), residues: 0 loop : -2.88 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 311 TYR 0.015 0.001 TYR A 244 PHE 0.009 0.001 PHE A 246 TRP 0.008 0.001 TRP A 134 HIS 0.007 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 3495) covalent geometry : angle 0.55498 / 0.28 ( 4779) SS BOND : bond 0.00120 / 0.06 ( 1) SS BOND : angle 0.32359 / 0.17 ( 2) hydrogen bonds : bond 0.05226 / 3.42 ( 194) hydrogen bonds : angle 4.11797 / 3.01 ( 558) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7092 (mp) REVERT: A 103 GLU cc_start: 0.8009 (tp30) cc_final: 0.7732 (tp30) REVERT: A 127 ASP cc_start: 0.8442 (t70) cc_final: 0.8061 (t0) REVERT: A 296 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8507 (pp) REVERT: A 356 ARG cc_start: 0.7643 (mtm180) cc_final: 0.7391 (mtm180) outliers start: 11 outliers final: 7 residues processed: 55 average time/residue: 0.0820 time to fit residues: 5.4913 Evaluate side-chains 57 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 455 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 37 optimal weight: 0.0050 chunk 24 optimal weight: 0.0000 chunk 14 optimal weight: 5.9990 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.159406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.115947 restraints weight = 3873.695| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.27 r_work: 0.3185 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3496 Z= 0.100 Angle : 0.516 10.191 4781 Z= 0.257 Chirality : 0.037 0.129 531 Planarity : 0.005 0.069 579 Dihedral : 4.767 55.308 461 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.94 % Allowed : 17.35 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.42), residues: 426 helix: 1.00 (0.31), residues: 297 sheet: None (None), residues: 0 loop : -2.69 (0.51), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 105 TYR 0.009 0.001 TYR A 101 PHE 0.006 0.001 PHE A 291 TRP 0.006 0.001 TRP A 122 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 ( 3495) covalent geometry : angle 0.51638 / 0.26 ( 4779) SS BOND : bond 0.00054 / 0.03 ( 1) SS BOND : angle 0.44464 / 0.25 ( 2) hydrogen bonds : bond 0.04016 / 2.63 ( 194) hydrogen bonds : angle 3.91447 / 2.86 ( 558) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6946 (mp) REVERT: A 103 GLU cc_start: 0.7918 (tp30) cc_final: 0.7623 (tp30) REVERT: A 127 ASP cc_start: 0.8353 (t70) cc_final: 0.7983 (t0) REVERT: A 181 CYS cc_start: 0.6909 (m) cc_final: 0.6451 (m) REVERT: A 356 ARG cc_start: 0.7470 (mtm180) cc_final: 0.7142 (mtm180) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.0747 time to fit residues: 4.9318 Evaluate side-chains 56 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 455 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 0.0670 chunk 40 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.155366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111266 restraints weight = 3950.607| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.29 r_work: 0.3123 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3496 Z= 0.131 Angle : 0.545 10.751 4781 Z= 0.273 Chirality : 0.038 0.128 531 Planarity : 0.005 0.075 579 Dihedral : 4.763 52.364 461 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.94 % Allowed : 17.94 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.41), residues: 426 helix: 1.02 (0.31), residues: 296 sheet: None (None), residues: 0 loop : -2.58 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 105 TYR 0.015 0.001 TYR A 244 PHE 0.009 0.001 PHE A 145 TRP 0.007 0.001 TRP A 134 HIS 0.002 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 3495) covalent geometry : angle 0.54439 / 0.27 ( 4779) SS BOND : bond 0.00286 / 0.15 ( 1) SS BOND : angle 1.28040 / 0.68 ( 2) hydrogen bonds : bond 0.05018 / 3.28 ( 194) hydrogen bonds : angle 4.00435 / 2.93 ( 558) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.6999 (mp) REVERT: A 127 ASP cc_start: 0.8390 (t70) cc_final: 0.8019 (t0) REVERT: A 181 CYS cc_start: 0.6970 (m) cc_final: 0.6482 (m) REVERT: A 356 ARG cc_start: 0.7581 (mtm180) cc_final: 0.6973 (mtm180) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.0656 time to fit residues: 4.4526 Evaluate side-chains 58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 455 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 1 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.155499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.111228 restraints weight = 3990.880| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.31 r_work: 0.3124 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3496 Z= 0.130 Angle : 0.559 12.591 4781 Z= 0.275 Chirality : 0.039 0.128 531 Planarity : 0.005 0.076 579 Dihedral : 4.710 50.010 461 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.94 % Allowed : 18.53 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.41), residues: 426 helix: 1.05 (0.31), residues: 296 sheet: None (None), residues: 0 loop : -2.50 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 105 TYR 0.013 0.001 TYR A 244 PHE 0.008 0.001 PHE A 145 TRP 0.006 0.001 TRP A 134 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 3495) covalent geometry : angle 0.55908 / 0.27 ( 4779) SS BOND : bond 0.00125 / 0.07 ( 1) SS BOND : angle 0.78975 / 0.43 ( 2) hydrogen bonds : bond 0.04894 / 3.19 ( 194) hydrogen bonds : angle 3.99330 / 2.91 ( 558) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6996 (mp) REVERT: A 127 ASP cc_start: 0.8383 (t70) cc_final: 0.8012 (t0) outliers start: 10 outliers final: 9 residues processed: 55 average time/residue: 0.0603 time to fit residues: 4.0572 Evaluate side-chains 59 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 455 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.154241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110056 restraints weight = 3940.270| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.28 r_work: 0.3107 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3496 Z= 0.147 Angle : 0.573 12.288 4781 Z= 0.286 Chirality : 0.039 0.129 531 Planarity : 0.005 0.075 579 Dihedral : 4.741 48.578 461 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.24 % Allowed : 18.82 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.41), residues: 426 helix: 1.00 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -2.32 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 356 TYR 0.016 0.001 TYR A 244 PHE 0.009 0.001 PHE A 145 TRP 0.007 0.001 TRP A 134 HIS 0.002 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 3495) covalent geometry : angle 0.57300 / 0.29 ( 4779) SS BOND : bond 0.00195 / 0.10 ( 1) SS BOND : angle 0.99947 / 0.54 ( 2) hydrogen bonds : bond 0.05245 / 3.42 ( 194) hydrogen bonds : angle 4.05540 / 2.96 ( 558) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7050 (mp) REVERT: A 127 ASP cc_start: 0.8389 (t70) cc_final: 0.8016 (t0) REVERT: A 356 ARG cc_start: 0.7651 (mtm180) cc_final: 0.7198 (mtm180) outliers start: 11 outliers final: 10 residues processed: 57 average time/residue: 0.0671 time to fit residues: 4.6059 Evaluate side-chains 62 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 455 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.156103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111889 restraints weight = 3924.955| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.29 r_work: 0.3140 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3496 Z= 0.119 Angle : 0.565 13.785 4781 Z= 0.278 Chirality : 0.038 0.128 531 Planarity : 0.005 0.074 579 Dihedral : 4.602 45.918 461 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.24 % Allowed : 19.12 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.42), residues: 426 helix: 1.12 (0.31), residues: 296 sheet: None (None), residues: 0 loop : -2.19 (0.55), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 105 TYR 0.010 0.001 TYR A 69 PHE 0.007 0.001 PHE A 145 TRP 0.007 0.001 TRP A 122 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 3495) covalent geometry : angle 0.56486 / 0.28 ( 4779) SS BOND : bond 0.00131 / 0.07 ( 1) SS BOND : angle 0.66434 / 0.36 ( 2) hydrogen bonds : bond 0.04648 / 3.03 ( 194) hydrogen bonds : angle 3.96779 / 2.89 ( 558) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: A 89 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7002 (mp) REVERT: A 127 ASP cc_start: 0.8367 (t70) cc_final: 0.7999 (t0) REVERT: A 356 ARG cc_start: 0.7660 (mtm180) cc_final: 0.7207 (mtm180) outliers start: 11 outliers final: 10 residues processed: 53 average time/residue: 0.0530 time to fit residues: 3.4641 Evaluate side-chains 58 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 455 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 0.0970 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.0570 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.158026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113827 restraints weight = 4004.264| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.31 r_work: 0.3142 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3496 Z= 0.117 Angle : 0.550 13.242 4781 Z= 0.271 Chirality : 0.038 0.130 531 Planarity : 0.005 0.073 579 Dihedral : 4.478 42.468 461 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.82 % Allowed : 18.82 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.42), residues: 426 helix: 1.18 (0.31), residues: 296 sheet: None (None), residues: 0 loop : -2.08 (0.57), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 105 TYR 0.011 0.001 TYR A 244 PHE 0.007 0.001 PHE A 291 TRP 0.006 0.001 TRP A 122 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 3495) covalent geometry : angle 0.55036 / 0.27 ( 4779) SS BOND : bond 0.00126 / 0.07 ( 1) SS BOND : angle 0.62763 / 0.34 ( 2) hydrogen bonds : bond 0.04503 / 2.95 ( 194) hydrogen bonds : angle 3.91897 / 2.86 ( 558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1059.55 seconds wall clock time: 18 minutes 43.39 seconds (1123.39 seconds total)