Starting phenix.real_space_refine on Sat Apr 4 21:14:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iu8_60893/04_2026/9iu8_60893.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iu8_60893/04_2026/9iu8_60893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iu8_60893/04_2026/9iu8_60893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iu8_60893/04_2026/9iu8_60893.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iu8_60893/04_2026/9iu8_60893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iu8_60893/04_2026/9iu8_60893.map" } resolution = 3.21 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= -0.000 sd= 0.037 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 Zn 1 6.06 5 P 50 5.49 5 S 10 5.16 5 C 2087 2.51 5 N 665 2.21 5 O 769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3582 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2556 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain breaks: 2 Chain: "E" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1299 SG CYS A 304 39.237 71.171 21.241 1.00229.33 S ATOM 1317 SG CYS A 307 39.849 68.304 19.028 1.00230.02 S ATOM 1468 SG CYS A 326 42.252 69.065 21.275 1.00223.79 S ATOM 1540 SG CYS A 335 41.923 71.881 18.609 1.00234.93 S Time building chain proxies: 0.68, per 1000 atoms: 0.19 Number of scatterers: 3582 At special positions: 0 Unit cell: (74.0773, 101.121, 63.4948, 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) Zn 1 29.99 S 10 16.00 P 50 15.00 O 769 8.00 N 665 7.00 C 2087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 108.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1000 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 304 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 307 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 326 " pdb="ZN ZN A1000 " - pdb=" SG CYS A 335 " Number of angles added : 6 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 588 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 5 sheets defined 49.5% alpha, 13.5% beta 25 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.631A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 209 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 242 through 246 Processing helix chain 'A' and resid 271 through 283 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 342 through 358 Processing helix chain 'A' and resid 371 through 388 removed outlier: 3.743A pdb=" N VAL A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 423 removed outlier: 3.679A pdb=" N LEU A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.782A pdb=" N GLU A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 459 Processing helix chain 'A' and resid 478 through 486 Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166 Processing sheet with id=AA2, first strand: chain 'A' and resid 249 through 250 Processing sheet with id=AA3, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 315 Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 368 removed outlier: 5.184A pdb=" N GLN A 437 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N GLU A 364 " --> pdb=" O THR A 435 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A 435 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 366 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG A 433 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 368 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU A 431 " --> pdb=" O VAL A 368 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 336 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 130 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 0.74 Time building geometry restraints manager: 0.45 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: 686 1.34 - 1.46: 1213 1.46 - 1.57: 1750 1.57 - 1.69: 98 1.69 - 1.81: 15 Bond restraints: 3762 Sorted by residual: bond pdb=" C LYS A 289 " pdb=" N PRO A 290 " ideal model delta sigma weight residual 1.329 1.362 -0.034 1.20e-02 6.94e+03 7.87e+00 bond pdb=" C GLU A 224 " pdb=" N PRO A 225 " ideal model delta sigma weight residual 1.332 1.366 -0.035 1.26e-02 6.30e+03 7.52e+00 bond pdb=" C THR A 294 " pdb=" N PRO A 295 " ideal model delta sigma weight residual 1.328 1.362 -0.034 1.26e-02 6.30e+03 7.08e+00 bond pdb=" C ARG A 426 " pdb=" N PRO A 427 " ideal model delta sigma weight residual 1.330 1.362 -0.032 1.25e-02 6.40e+03 6.56e+00 bond pdb=" C HIS A 321 " pdb=" N PRO A 322 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.31e-02 5.83e+03 6.53e+00 ... (remaining 3757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 4777 2.63 - 5.27: 489 5.27 - 7.90: 35 7.90 - 10.53: 3 10.53 - 13.17: 2 Bond angle restraints: 5306 Sorted by residual: angle pdb=" O3' DG F 32 " pdb=" P DT F 33 " pdb=" O5' DT F 33 " ideal model delta sigma weight residual 104.00 90.83 13.17 1.50e+00 4.44e-01 7.70e+01 angle pdb=" N ARG A 155 " pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " ideal model delta sigma weight residual 110.46 120.73 -10.27 1.57e+00 4.06e-01 4.28e+01 angle pdb=" C ARG A 155 " pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " ideal model delta sigma weight residual 109.72 98.91 10.81 1.92e+00 2.71e-01 3.17e+01 angle pdb=" O3' DC F 30 " pdb=" P DG F 31 " pdb=" O5' DG F 31 " ideal model delta sigma weight residual 104.00 111.94 -7.94 1.50e+00 4.44e-01 2.80e+01 angle pdb=" O3' DG E 23 " pdb=" P DC E 24 " pdb=" O5' DC E 24 " ideal model delta sigma weight residual 104.00 96.33 7.67 1.50e+00 4.44e-01 2.62e+01 ... (remaining 5301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 1605 16.02 - 32.05: 255 32.05 - 48.07: 130 48.07 - 64.09: 98 64.09 - 80.12: 12 Dihedral angle restraints: 2100 sinusoidal: 1188 harmonic: 912 Sorted by residual: dihedral pdb=" CA ARG A 155 " pdb=" C ARG A 155 " pdb=" N GLY A 156 " pdb=" CA GLY A 156 " ideal model delta harmonic sigma weight residual -180.00 -159.20 -20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PRO A 197 " pdb=" C PRO A 197 " pdb=" N LEU A 198 " pdb=" CA LEU A 198 " ideal model delta harmonic sigma weight residual -180.00 -160.67 -19.33 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C ARG A 155 " pdb=" N ARG A 155 " pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " ideal model delta harmonic sigma weight residual -122.60 -113.31 -9.29 0 2.50e+00 1.60e-01 1.38e+01 ... (remaining 2097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 505 0.128 - 0.256: 63 0.256 - 0.384: 2 0.384 - 0.513: 1 0.513 - 0.641: 2 Chirality restraints: 573 Sorted by residual: chirality pdb=" P DC F 28 " pdb=" OP1 DC F 28 " pdb=" OP2 DC F 28 " pdb=" O5' DC F 28 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P DG E 1 " pdb=" OP1 DG E 1 " pdb=" OP2 DG E 1 " pdb=" O5' DG E 1 " both_signs ideal model delta sigma weight residual True 2.35 2.96 -0.61 2.00e-01 2.50e+01 9.33e+00 chirality pdb=" P DG F 31 " pdb=" OP1 DG F 31 " pdb=" OP2 DG F 31 " pdb=" O5' DG F 31 " both_signs ideal model delta sigma weight residual True 2.35 -2.74 -0.40 2.00e-01 2.50e+01 3.95e+00 ... (remaining 570 not shown) Planarity restraints: 516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 237 " 0.349 9.50e-02 1.11e+02 1.57e-01 1.75e+01 pdb=" NE ARG A 237 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 237 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 237 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 237 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 173 " 0.297 9.50e-02 1.11e+02 1.34e-01 1.32e+01 pdb=" NE ARG A 173 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 173 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 173 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 173 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG F 35 " -0.042 2.00e-02 2.50e+03 1.81e-02 9.86e+00 pdb=" N9 DG F 35 " 0.041 2.00e-02 2.50e+03 pdb=" C8 DG F 35 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG F 35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG F 35 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG F 35 " -0.009 2.00e-02 2.50e+03 pdb=" O6 DG F 35 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG F 35 " -0.006 2.00e-02 2.50e+03 pdb=" C2 DG F 35 " -0.006 2.00e-02 2.50e+03 pdb=" N2 DG F 35 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG F 35 " 0.016 2.00e-02 2.50e+03 pdb=" C4 DG F 35 " 0.008 2.00e-02 2.50e+03 ... (remaining 513 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 585 2.81 - 3.33: 3165 3.33 - 3.85: 6633 3.85 - 4.38: 7511 4.38 - 4.90: 11492 Nonbonded interactions: 29386 Sorted by model distance: nonbonded pdb=" OG SER A 157 " pdb=" O2 DC E 22 " model vdw 2.283 3.040 nonbonded pdb=" OG SER A 212 " pdb=" OP1 DG F 35 " model vdw 2.396 3.040 nonbonded pdb=" NH1 ARG A 183 " pdb=" OE1 GLU A 186 " model vdw 2.459 3.120 nonbonded pdb=" O4' DC E 22 " pdb=" O2 DC E 22 " model vdw 2.499 3.040 nonbonded pdb=" O5' DG F 34 " pdb=" O4' DG F 34 " model vdw 2.526 2.432 ... (remaining 29381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.150 Find NCS groups from input model: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5221 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 : 0.009 0.044 3766 Z= 0.520 Angle : 1.666 16.813 5312 Z= 1.042 Chirality : 0.087 0.641 573 Planarity : 0.018 0.157 516 Dihedral : 22.314 80.118 1512 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.26 % Allowed : 4.53 % Favored : 93.21 % Cbeta Deviations : 0.34 % 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: -1.91 (0.40), residues: 313 helix: -1.25 (0.36), residues: 136 sheet: -1.33 (0.75), residues: 37 loop : -1.09 (0.46), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.005 ARG A 237 TYR 0.020 0.005 TYR A 312 PHE 0.024 0.003 PHE A 217 TRP 0.015 0.002 TRP A 161 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00904 ( 3762) covalent geometry : angle 1.63194 ( 5306) hydrogen bonds : bond 0.17419 ( 185) hydrogen bonds : angle 6.90061 ( 466) metal coordination : bond 0.01390 ( 4) metal coordination : angle 10.04885 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.116 Fit side-chains REVERT: A 155 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6107 (ttp-110) REVERT: A 272 ARG cc_start: 0.5015 (ttp-110) cc_final: 0.4472 (ttm-80) REVERT: A 294 THR cc_start: 0.7699 (m) cc_final: 0.7468 (p) REVERT: A 324 TYR cc_start: 0.5490 (m-80) cc_final: 0.5237 (m-80) REVERT: A 371 SER cc_start: 0.6115 (t) cc_final: 0.5804 (m) REVERT: A 420 LEU cc_start: 0.5522 (mt) cc_final: 0.5319 (mt) REVERT: A 434 GLU cc_start: 0.7869 (mt-10) cc_final: 0.6820 (mm-30) REVERT: A 474 ILE cc_start: 0.7350 (mp) cc_final: 0.7136 (mp) outliers start: 6 outliers final: 2 residues processed: 47 average time/residue: 0.1189 time to fit residues: 6.3518 Evaluate side-chains 31 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 463 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.0970 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.213845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.146196 restraints weight = 4009.532| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.09 r_work: 0.3428 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 3766 Z= 0.278 Angle : 0.671 8.198 5312 Z= 0.370 Chirality : 0.040 0.165 573 Planarity : 0.006 0.057 516 Dihedral : 25.860 85.663 897 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.26 % Allowed : 9.06 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.46), residues: 313 helix: 1.37 (0.43), residues: 140 sheet: -0.83 (0.59), residues: 63 loop : -0.22 (0.58), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 223 TYR 0.017 0.003 TYR A 482 PHE 0.012 0.002 PHE A 464 TRP 0.014 0.002 TRP A 442 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00633 ( 3762) covalent geometry : angle 0.65679 ( 5306) hydrogen bonds : bond 0.04538 ( 185) hydrogen bonds : angle 4.06511 ( 466) metal coordination : bond 0.00899 ( 4) metal coordination : angle 4.09814 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.092 Fit side-chains REVERT: A 155 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7969 (ttp-110) REVERT: A 226 GLN cc_start: 0.7612 (mp10) cc_final: 0.7226 (mp10) REVERT: A 272 ARG cc_start: 0.8188 (ttp-110) cc_final: 0.7209 (ttm-80) REVERT: A 371 SER cc_start: 0.7745 (t) cc_final: 0.7316 (m) REVERT: A 463 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7410 (t) outliers start: 6 outliers final: 3 residues processed: 33 average time/residue: 0.0817 time to fit residues: 3.2224 Evaluate side-chains 29 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 463 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.0470 chunk 5 optimal weight: 0.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.224936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.165018 restraints weight = 3897.391| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.94 r_work: 0.3539 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3766 Z= 0.177 Angle : 0.566 8.915 5312 Z= 0.316 Chirality : 0.035 0.133 573 Planarity : 0.004 0.036 516 Dihedral : 25.510 84.843 897 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.51 % Allowed : 9.81 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.48), residues: 313 helix: 2.28 (0.43), residues: 140 sheet: -0.88 (0.68), residues: 49 loop : 0.43 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 223 TYR 0.014 0.002 TYR A 482 PHE 0.009 0.001 PHE A 314 TRP 0.010 0.001 TRP A 345 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 3762) covalent geometry : angle 0.56081 ( 5306) hydrogen bonds : bond 0.03410 ( 185) hydrogen bonds : angle 3.75786 ( 466) metal coordination : bond 0.00561 ( 4) metal coordination : angle 2.39020 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.107 Fit side-chains REVERT: A 155 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7423 (ttp80) REVERT: A 226 GLN cc_start: 0.7608 (mp10) cc_final: 0.7309 (mp10) REVERT: A 272 ARG cc_start: 0.8271 (ttp-110) cc_final: 0.7386 (ttm-80) REVERT: A 371 SER cc_start: 0.7523 (t) cc_final: 0.7056 (m) REVERT: A 434 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7549 (mm-30) outliers start: 4 outliers final: 1 residues processed: 30 average time/residue: 0.1058 time to fit residues: 3.7291 Evaluate side-chains 27 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.214431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.148660 restraints weight = 3882.917| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.91 r_work: 0.3454 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3766 Z= 0.229 Angle : 0.599 8.903 5312 Z= 0.329 Chirality : 0.036 0.161 573 Planarity : 0.004 0.033 516 Dihedral : 25.631 87.939 896 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.64 % Allowed : 8.30 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.48), residues: 313 helix: 2.40 (0.43), residues: 140 sheet: -0.96 (0.66), residues: 49 loop : 0.52 (0.58), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.015 0.002 TYR A 154 PHE 0.010 0.002 PHE A 464 TRP 0.010 0.001 TRP A 345 HIS 0.003 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 3762) covalent geometry : angle 0.58948 ( 5306) hydrogen bonds : bond 0.03650 ( 185) hydrogen bonds : angle 3.80607 ( 466) metal coordination : bond 0.00858 ( 4) metal coordination : angle 3.14265 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 26 time to evaluate : 0.079 Fit side-chains REVERT: A 155 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7566 (ptt90) REVERT: A 226 GLN cc_start: 0.7676 (mp10) cc_final: 0.7344 (mp10) REVERT: A 272 ARG cc_start: 0.8272 (ttp-110) cc_final: 0.7329 (ttm-80) outliers start: 7 outliers final: 5 residues processed: 31 average time/residue: 0.0981 time to fit residues: 3.6119 Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.214893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.149274 restraints weight = 3926.633| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.94 r_work: 0.3460 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3766 Z= 0.189 Angle : 0.563 9.753 5312 Z= 0.311 Chirality : 0.034 0.130 573 Planarity : 0.004 0.031 516 Dihedral : 25.499 86.402 896 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.26 % Allowed : 9.06 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.48), residues: 313 helix: 2.54 (0.43), residues: 140 sheet: -0.82 (0.67), residues: 51 loop : 0.58 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 416 TYR 0.014 0.002 TYR A 154 PHE 0.008 0.001 PHE A 314 TRP 0.009 0.001 TRP A 345 HIS 0.004 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 3762) covalent geometry : angle 0.55683 ( 5306) hydrogen bonds : bond 0.03315 ( 185) hydrogen bonds : angle 3.70045 ( 466) metal coordination : bond 0.00732 ( 4) metal coordination : angle 2.60819 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.111 Fit side-chains REVERT: A 155 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7488 (ptt90) REVERT: A 226 GLN cc_start: 0.7690 (mp10) cc_final: 0.7381 (mp10) REVERT: A 272 ARG cc_start: 0.8228 (ttp-110) cc_final: 0.7276 (ttm-80) outliers start: 6 outliers final: 4 residues processed: 31 average time/residue: 0.0915 time to fit residues: 3.3994 Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 26 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.214791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.149684 restraints weight = 3953.452| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.05 r_work: 0.3469 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3766 Z= 0.188 Angle : 0.566 10.388 5312 Z= 0.311 Chirality : 0.034 0.135 573 Planarity : 0.004 0.029 516 Dihedral : 25.430 86.485 895 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.64 % Allowed : 10.19 % Favored : 87.17 % 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: 1.87 (0.49), residues: 313 helix: 2.58 (0.44), residues: 140 sheet: -0.71 (0.69), residues: 51 loop : 0.68 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.015 0.002 TYR A 154 PHE 0.008 0.001 PHE A 314 TRP 0.009 0.001 TRP A 345 HIS 0.005 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 3762) covalent geometry : angle 0.56011 ( 5306) hydrogen bonds : bond 0.03272 ( 185) hydrogen bonds : angle 3.71442 ( 466) metal coordination : bond 0.00741 ( 4) metal coordination : angle 2.46663 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.095 Fit side-chains REVERT: A 155 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7759 (ttp-110) REVERT: A 226 GLN cc_start: 0.7700 (mp10) cc_final: 0.7403 (mp10) REVERT: A 272 ARG cc_start: 0.8272 (ttp-110) cc_final: 0.7337 (ttm-80) REVERT: A 417 GLN cc_start: 0.6996 (pt0) cc_final: 0.4930 (tp-100) outliers start: 7 outliers final: 6 residues processed: 33 average time/residue: 0.0781 time to fit residues: 3.1230 Evaluate side-chains 35 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 24 optimal weight: 0.0670 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.0070 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.226540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.167640 restraints weight = 4016.131| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.95 r_work: 0.3600 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3766 Z= 0.136 Angle : 0.520 10.400 5312 Z= 0.290 Chirality : 0.032 0.115 573 Planarity : 0.003 0.026 516 Dihedral : 25.106 85.925 895 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.89 % Allowed : 12.08 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.49), residues: 313 helix: 2.75 (0.44), residues: 141 sheet: -0.50 (0.69), residues: 53 loop : 0.90 (0.60), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.011 0.001 TYR A 154 PHE 0.007 0.001 PHE A 314 TRP 0.009 0.001 TRP A 345 HIS 0.004 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 3762) covalent geometry : angle 0.51600 ( 5306) hydrogen bonds : bond 0.02880 ( 185) hydrogen bonds : angle 3.56199 ( 466) metal coordination : bond 0.00460 ( 4) metal coordination : angle 1.86452 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.106 Fit side-chains REVERT: A 153 LYS cc_start: 0.8439 (mmtp) cc_final: 0.8206 (mttm) REVERT: A 155 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7340 (ttp80) REVERT: A 226 GLN cc_start: 0.7699 (mp10) cc_final: 0.7465 (mp10) REVERT: A 272 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7267 (tpp-160) REVERT: A 417 GLN cc_start: 0.6748 (pt0) cc_final: 0.4781 (tp40) REVERT: A 434 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7575 (mm-30) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 0.0838 time to fit residues: 3.6730 Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.214825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148966 restraints weight = 3994.276| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.83 r_work: 0.3511 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3766 Z= 0.191 Angle : 0.567 10.774 5312 Z= 0.313 Chirality : 0.035 0.138 573 Planarity : 0.004 0.029 516 Dihedral : 25.293 86.062 895 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.89 % Allowed : 13.96 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.00 (0.48), residues: 313 helix: 2.50 (0.44), residues: 141 sheet: -0.41 (0.69), residues: 53 loop : 0.89 (0.59), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.014 0.002 TYR A 154 PHE 0.008 0.001 PHE A 314 TRP 0.007 0.001 TRP A 345 HIS 0.004 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 3762) covalent geometry : angle 0.56240 ( 5306) hydrogen bonds : bond 0.03247 ( 185) hydrogen bonds : angle 3.70825 ( 466) metal coordination : bond 0.00727 ( 4) metal coordination : angle 2.31535 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.101 Fit side-chains REVERT: A 155 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7629 (ttp80) REVERT: A 226 GLN cc_start: 0.7821 (mp10) cc_final: 0.7505 (mp10) REVERT: A 272 ARG cc_start: 0.8346 (ttp-110) cc_final: 0.7277 (tpp-160) REVERT: A 417 GLN cc_start: 0.6945 (pt0) cc_final: 0.4925 (tp-100) outliers start: 5 outliers final: 3 residues processed: 31 average time/residue: 0.0837 time to fit residues: 3.0749 Evaluate side-chains 31 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 0.0060 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.215253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.159753 restraints weight = 3959.166| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.74 r_work: 0.3502 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3766 Z= 0.180 Angle : 0.561 11.174 5312 Z= 0.309 Chirality : 0.034 0.128 573 Planarity : 0.004 0.029 516 Dihedral : 25.293 86.080 895 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.89 % Allowed : 13.21 % 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 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: 2.05 (0.48), residues: 313 helix: 2.50 (0.43), residues: 141 sheet: -0.32 (0.69), residues: 53 loop : 0.93 (0.59), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.014 0.002 TYR A 154 PHE 0.008 0.001 PHE A 314 TRP 0.008 0.001 TRP A 345 HIS 0.004 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 3762) covalent geometry : angle 0.55623 ( 5306) hydrogen bonds : bond 0.03167 ( 185) hydrogen bonds : angle 3.72120 ( 466) metal coordination : bond 0.00692 ( 4) metal coordination : angle 2.27860 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.115 Fit side-chains REVERT: A 155 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7562 (ttp80) REVERT: A 226 GLN cc_start: 0.7856 (mp10) cc_final: 0.7547 (mp10) REVERT: A 272 ARG cc_start: 0.8309 (ttp-110) cc_final: 0.7228 (tpp-160) REVERT: A 417 GLN cc_start: 0.6637 (pt0) cc_final: 0.4566 (tp-100) outliers start: 5 outliers final: 4 residues processed: 29 average time/residue: 0.1014 time to fit residues: 3.4973 Evaluate side-chains 29 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.211430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.145606 restraints weight = 3991.246| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.01 r_work: 0.3407 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 3766 Z= 0.303 Angle : 0.663 11.990 5312 Z= 0.358 Chirality : 0.040 0.193 573 Planarity : 0.005 0.039 516 Dihedral : 25.771 89.579 895 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.26 % Allowed : 13.21 % Favored : 84.53 % 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: 1.84 (0.48), residues: 313 helix: 2.22 (0.43), residues: 141 sheet: -0.48 (0.69), residues: 51 loop : 0.97 (0.60), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 223 TYR 0.016 0.002 TYR A 154 PHE 0.011 0.002 PHE A 464 TRP 0.008 0.001 TRP A 442 HIS 0.004 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00697 ( 3762) covalent geometry : angle 0.65478 ( 5306) hydrogen bonds : bond 0.04054 ( 185) hydrogen bonds : angle 3.97884 ( 466) metal coordination : bond 0.01143 ( 4) metal coordination : angle 3.09929 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 626 Ramachandran restraints generated. 313 Oldfield, 0 Emsley, 313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.079 Fit side-chains REVERT: A 155 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7816 (ptt90) REVERT: A 272 ARG cc_start: 0.8507 (ttp-110) cc_final: 0.7484 (ttm-80) REVERT: A 417 GLN cc_start: 0.6956 (pt0) cc_final: 0.4912 (tp-100) REVERT: A 434 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7668 (mm-30) outliers start: 6 outliers final: 5 residues processed: 29 average time/residue: 0.0974 time to fit residues: 3.3357 Evaluate side-chains 31 residues out of total 265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.214736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.152206 restraints weight = 3933.029| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.86 r_work: 0.3471 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3766 Z= 0.177 Angle : 0.574 12.320 5312 Z= 0.315 Chirality : 0.034 0.128 573 Planarity : 0.004 0.032 516 Dihedral : 25.500 86.545 895 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.26 % Allowed : 12.83 % 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 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: 2.09 (0.48), residues: 313 helix: 2.48 (0.43), residues: 141 sheet: -0.38 (0.69), residues: 51 loop : 1.04 (0.60), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 444 TYR 0.013 0.002 TYR A 154 PHE 0.008 0.001 PHE A 314 TRP 0.009 0.001 TRP A 345 HIS 0.005 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 3762) covalent geometry : angle 0.56932 ( 5306) hydrogen bonds : bond 0.03240 ( 185) hydrogen bonds : angle 3.77922 ( 466) metal coordination : bond 0.00684 ( 4) metal coordination : angle 2.33502 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1198.08 seconds wall clock time: 21 minutes 2.77 seconds (1262.77 seconds total)