Starting phenix.real_space_refine on Wed Aug 5 10:24:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nzq_49956/08_2026/9nzq_49956.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nzq_49956/08_2026/9nzq_49956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nzq_49956/08_2026/9nzq_49956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nzq_49956/08_2026/9nzq_49956.map" model { file = "/net/cci-nas-00/data/ceres_data/9nzq_49956/08_2026/9nzq_49956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nzq_49956/08_2026/9nzq_49956.cif" } resolution = 3.67 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= 0.013 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 152 5.49 5 S 40 5.16 5 C 5258 2.51 5 N 1677 2.21 5 O 2130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9258 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3386 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 11, 'TRANS': 411} Chain: "B" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2629 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 9, 'TRANS': 317} Chain breaks: 5 Chain: "C" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 331 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "E" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2748 Classifications: {'RNA': 128} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 10, 'rna3p_pur': 60, 'rna3p_pyr': 44} Link IDs: {'rna2p': 24, 'rna3p': 103} Chain breaks: 1 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 3013 SG CYS A 377 18.032 83.772 72.324 1.00 55.33 S ATOM 3036 SG CYS A 380 14.978 86.360 70.972 1.00 65.53 S ATOM 3157 SG CYS A 396 18.685 87.212 70.940 1.00 62.24 S ATOM 3179 SG CYS A 399 16.933 86.920 74.005 1.00 58.21 S Time building chain proxies: 1.88, per 1000 atoms: 0.20 Number of scatterers: 9258 At special positions: 0 Unit cell: (94, 111.86, 121.26, 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 40 16.00 P 152 15.00 O 2130 8.00 N 1677 7.00 C 5258 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: 0.74 Conformation dependent library (CDL) restraints added in 136.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 399 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 396 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 380 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 377 " Number of angles added : 6 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 7 sheets defined 50.9% alpha, 7.2% beta 43 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 25 through 62 Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.801A pdb=" N GLU A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.747A pdb=" N HIS A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN A 88 " --> pdb=" O CYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 111 removed outlier: 3.598A pdb=" N LYS A 107 " --> pdb=" O LYS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 156 through 162 Processing helix chain 'A' and resid 178 through 188 removed outlier: 4.155A pdb=" N PHE A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 271 removed outlier: 3.631A pdb=" N ALA A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 271 " --> pdb=" O MET A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 319 Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.596A pdb=" N ARG A 388 " --> pdb=" O LYS A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 415 Processing helix chain 'A' and resid 417 through 427 removed outlier: 3.840A pdb=" N ILE A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 54 Processing helix chain 'B' and resid 77 through 89 Processing helix chain 'B' and resid 93 through 111 Processing helix chain 'B' and resid 111 through 117 Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 178 through 188 removed outlier: 3.883A pdb=" N PHE B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 274 Processing helix chain 'B' and resid 294 through 319 Processing helix chain 'B' and resid 346 through 361 removed outlier: 3.822A pdb=" N LEU B 350 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 415 removed outlier: 3.677A pdb=" N ILE B 415 " --> pdb=" O GLN B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 3.504A pdb=" N PHE A 205 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 197 " --> pdb=" O PHE A 207 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 198 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 131 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 141 removed outlier: 3.691A pdb=" N ILE A 148 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 237 removed outlier: 3.598A pdb=" N LEU A 235 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 140 Processing sheet with id=AA6, first strand: chain 'B' and resid 226 through 230 removed outlier: 5.115A pdb=" N GLY B 230 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ALA B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 327 removed outlier: 3.670A pdb=" N VAL B 366 " --> pdb=" O ILE B 324 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 110 hydrogen bonds 212 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 83 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1366 1.32 - 1.45: 3457 1.45 - 1.57: 4577 1.57 - 1.70: 301 1.70 - 1.82: 61 Bond restraints: 9762 Sorted by residual: bond pdb=" N9 A E 40 " pdb=" C4 A E 40 " ideal model delta sigma weight residual 1.374 1.396 -0.022 6.00e-03 2.78e+04 1.32e+01 bond pdb=" N9 A E 69 " pdb=" C4 A E 69 " ideal model delta sigma weight residual 1.374 1.395 -0.021 6.00e-03 2.78e+04 1.22e+01 bond pdb=" N9 A E 99 " pdb=" C4 A E 99 " ideal model delta sigma weight residual 1.374 1.395 -0.021 6.00e-03 2.78e+04 1.20e+01 bond pdb=" N9 A E 65 " pdb=" C4 A E 65 " ideal model delta sigma weight residual 1.374 1.392 -0.018 6.00e-03 2.78e+04 9.17e+00 bond pdb=" N9 A E 83 " pdb=" C4 A E 83 " ideal model delta sigma weight residual 1.374 1.391 -0.017 6.00e-03 2.78e+04 8.43e+00 ... (remaining 9757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 13079 2.56 - 5.11: 663 5.11 - 7.67: 106 7.67 - 10.22: 25 10.22 - 12.78: 12 Bond angle restraints: 13885 Sorted by residual: angle pdb=" N1 C E 66 " pdb=" C2 C E 66 " pdb=" O2 C E 66 " ideal model delta sigma weight residual 118.90 124.36 -5.46 6.00e-01 2.78e+00 8.27e+01 angle pdb=" N MET B 26 " pdb=" CA MET B 26 " pdb=" CB MET B 26 " ideal model delta sigma weight residual 110.01 120.25 -10.24 1.45e+00 4.76e-01 4.99e+01 angle pdb=" C1' C E 66 " pdb=" N1 C E 66 " pdb=" C2 C E 66 " ideal model delta sigma weight residual 118.80 126.46 -7.66 1.10e+00 8.26e-01 4.85e+01 angle pdb=" C3' U E 140 " pdb=" O3' U E 140 " pdb=" P G E 141 " ideal model delta sigma weight residual 119.70 127.87 -8.17 1.20e+00 6.94e-01 4.63e+01 angle pdb=" O2 C E 66 " pdb=" C2 C E 66 " pdb=" N3 C E 66 " ideal model delta sigma weight residual 121.90 117.30 4.60 7.00e-01 2.04e+00 4.32e+01 ... (remaining 13880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.77: 5269 32.77 - 65.54: 643 65.54 - 98.32: 54 98.32 - 131.09: 5 131.09 - 163.86: 8 Dihedral angle restraints: 5979 sinusoidal: 3796 harmonic: 2183 Sorted by residual: dihedral pdb=" C5' U E 140 " pdb=" C4' U E 140 " pdb=" C3' U E 140 " pdb=" O3' U E 140 " ideal model delta sinusoidal sigma weight residual 147.00 80.88 66.12 1 8.00e+00 1.56e-02 8.93e+01 dihedral pdb=" C4' U E 140 " pdb=" C3' U E 140 " pdb=" C2' U E 140 " pdb=" C1' U E 140 " ideal model delta sinusoidal sigma weight residual -35.00 28.90 -63.90 1 8.00e+00 1.56e-02 8.40e+01 dihedral pdb=" O4' C E 19 " pdb=" C1' C E 19 " pdb=" N1 C E 19 " pdb=" C2 C E 19 " ideal model delta sinusoidal sigma weight residual 200.00 45.28 154.72 1 1.50e+01 4.44e-03 8.12e+01 ... (remaining 5976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1223 0.073 - 0.146: 346 0.146 - 0.220: 39 0.220 - 0.293: 8 0.293 - 0.366: 3 Chirality restraints: 1619 Sorted by residual: chirality pdb=" CA MET B 26 " pdb=" N MET B 26 " pdb=" C MET B 26 " pdb=" CB MET B 26 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CB ILE B 324 " pdb=" CA ILE B 324 " pdb=" CG1 ILE B 324 " pdb=" CG2 ILE B 324 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C3' U E 140 " pdb=" C4' U E 140 " pdb=" O3' U E 140 " pdb=" C2' U E 140 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 1616 not shown) Planarity restraints: 1207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G E 127 " 0.031 2.00e-02 2.50e+03 2.76e-02 2.29e+01 pdb=" N9 G E 127 " -0.031 2.00e-02 2.50e+03 pdb=" C8 G E 127 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G E 127 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G E 127 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G E 127 " -0.018 2.00e-02 2.50e+03 pdb=" O6 G E 127 " 0.021 2.00e-02 2.50e+03 pdb=" N1 G E 127 " 0.016 2.00e-02 2.50e+03 pdb=" C2 G E 127 " -0.069 2.00e-02 2.50e+03 pdb=" N2 G E 127 " 0.037 2.00e-02 2.50e+03 pdb=" N3 G E 127 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G E 127 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 407 " 0.025 2.00e-02 2.50e+03 2.77e-02 1.34e+01 pdb=" CG PHE A 407 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE A 407 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 407 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 407 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 407 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 407 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 240 " 0.018 2.00e-02 2.50e+03 2.66e-02 1.23e+01 pdb=" CG PHE B 240 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE B 240 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B 240 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 240 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 240 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 240 " -0.000 2.00e-02 2.50e+03 ... (remaining 1204 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 3559 2.93 - 3.42: 9246 3.42 - 3.91: 17099 3.91 - 4.41: 18315 4.41 - 4.90: 26932 Nonbonded interactions: 75151 Sorted by model distance: nonbonded pdb=" N1 A E 34 " pdb=" O6 G E 64 " model vdw 2.434 2.496 nonbonded pdb=" O4' C E 70 " pdb=" C6 C E 70 " model vdw 2.481 2.672 nonbonded pdb=" O5' G E 116 " pdb=" O4' G E 116 " model vdw 2.519 2.432 nonbonded pdb=" O4' C E 66 " pdb=" C6 C E 66 " model vdw 2.526 2.672 nonbonded pdb=" N ARG B 201 " pdb=" O ARG B 201 " model vdw 2.527 2.496 ... (remaining 75146 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 group one per residue 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: 2.170 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 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 0.098 9766 Z= 0.405 Angle : 1.306 18.404 13891 Z= 0.908 Chirality : 0.068 0.366 1619 Planarity : 0.010 0.100 1207 Dihedral : 24.090 163.859 4573 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.09 % Allowed : 28.68 % Favored : 70.23 % Cbeta Deviations : 0.14 % 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: -1.43 (0.30), residues: 736 helix: 0.49 (0.27), residues: 347 sheet: -2.25 (0.48), residues: 117 loop : -2.20 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.004 ARG B 76 TYR 0.034 0.003 TYR A 125 PHE 0.064 0.005 PHE A 407 TRP 0.033 0.003 TRP A 51 HIS 0.021 0.002 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.40 ( 9762) covalent geometry : angle 1.29264 / 0.91 (13885) hydrogen bonds : bond 0.14312 / 9.50 ( 415) hydrogen bonds : angle 5.62870 / 4.04 ( 1109) metal coordination : bond 0.01799 / 0.89 ( 4) metal coordination : angle 9.04006 / 3.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.7493 (t0) cc_final: 0.6938 (t0) outliers start: 7 outliers final: 3 residues processed: 81 average time/residue: 0.1072 time to fit residues: 11.5476 Evaluate side-chains 59 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 372 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN A 320 GLN A 372 HIS A 391 GLN A 411 GLN A 412 ASN B 25 ASN B 80 HIS B 184 ASN B 217 HIS ** B 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.070965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.053282 restraints weight = 51402.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.055026 restraints weight = 23895.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.056090 restraints weight = 15595.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.056584 restraints weight = 12311.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.057014 restraints weight = 10997.817| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 9766 Z= 0.276 Angle : 0.800 12.511 13891 Z= 0.428 Chirality : 0.047 0.503 1619 Planarity : 0.006 0.078 1207 Dihedral : 24.782 165.434 3083 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.43 % Allowed : 24.65 % Favored : 69.92 % 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: -0.45 (0.31), residues: 736 helix: 1.40 (0.27), residues: 353 sheet: -1.83 (0.48), residues: 124 loop : -1.89 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 301 TYR 0.023 0.002 TYR B 315 PHE 0.026 0.003 PHE B 300 TRP 0.022 0.003 TRP A 51 HIS 0.007 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.28 ( 9762) covalent geometry : angle 0.79105 / 0.43 (13885) hydrogen bonds : bond 0.06886 / 4.56 ( 415) hydrogen bonds : angle 4.66990 / 3.40 ( 1109) metal coordination : bond 0.02035 / 0.95 ( 4) metal coordination : angle 5.82566 / 2.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 59 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8602 (mp) REVERT: A 121 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8119 (p) REVERT: A 212 PHE cc_start: 0.7101 (OUTLIER) cc_final: 0.6780 (m-10) REVERT: A 314 ASP cc_start: 0.8531 (m-30) cc_final: 0.8313 (m-30) REVERT: A 371 ARG cc_start: 0.8351 (tpt90) cc_final: 0.8054 (tpt90) REVERT: A 410 SER cc_start: 0.9047 (OUTLIER) cc_final: 0.8438 (t) REVERT: B 16 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.6949 (p90) REVERT: B 26 MET cc_start: 0.8842 (mpp) cc_final: 0.8485 (mpp) REVERT: B 306 HIS cc_start: 0.9656 (OUTLIER) cc_final: 0.9397 (t-90) REVERT: B 372 HIS cc_start: 0.7436 (t70) cc_final: 0.7207 (t70) outliers start: 35 outliers final: 13 residues processed: 91 average time/residue: 0.0842 time to fit residues: 10.9983 Evaluate side-chains 75 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 372 HIS Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 16 TYR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 306 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 0.0050 chunk 73 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 77 optimal weight: 10.0000 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS B 273 HIS ** B 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.071964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.054375 restraints weight = 50896.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.056178 restraints weight = 23653.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.057281 restraints weight = 15389.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.057891 restraints weight = 12111.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.058281 restraints weight = 10673.228| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9766 Z= 0.139 Angle : 0.655 12.579 13891 Z= 0.355 Chirality : 0.041 0.512 1619 Planarity : 0.004 0.050 1207 Dihedral : 24.671 167.885 3081 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.95 % Allowed : 27.75 % Favored : 69.30 % 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 (0.31), residues: 736 helix: 1.79 (0.26), residues: 355 sheet: -1.56 (0.49), residues: 119 loop : -1.86 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 201 TYR 0.015 0.002 TYR A 125 PHE 0.012 0.002 PHE B 300 TRP 0.014 0.001 TRP A 51 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 ( 9762) covalent geometry : angle 0.64255 / 0.35 (13885) hydrogen bonds : bond 0.06167 / 4.00 ( 415) hydrogen bonds : angle 4.14295 / 3.01 ( 1109) metal coordination : bond 0.01051 / 0.51 ( 4) metal coordination : angle 6.07011 / 2.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8588 (mp) REVERT: A 145 ARG cc_start: 0.8812 (tpt90) cc_final: 0.8429 (tpt-90) REVERT: A 186 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7970 (mtm) REVERT: A 210 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: A 314 ASP cc_start: 0.8482 (m-30) cc_final: 0.8243 (m-30) REVERT: A 345 TRP cc_start: 0.9055 (t-100) cc_final: 0.8845 (t-100) REVERT: B 16 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.6932 (p90) REVERT: B 26 MET cc_start: 0.8825 (mpp) cc_final: 0.8117 (mpp) REVERT: B 306 HIS cc_start: 0.9624 (OUTLIER) cc_final: 0.9380 (t-90) REVERT: B 372 HIS cc_start: 0.7352 (t70) cc_final: 0.7103 (t70) outliers start: 19 outliers final: 9 residues processed: 72 average time/residue: 0.0931 time to fit residues: 9.3248 Evaluate side-chains 67 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 372 HIS Chi-restraints excluded: chain B residue 16 TYR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 306 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 82 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN A 412 ASN B 80 HIS B 372 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.069792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.051977 restraints weight = 51958.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.053753 restraints weight = 23836.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.054822 restraints weight = 15500.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.055445 restraints weight = 12236.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.055721 restraints weight = 10774.554| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9766 Z= 0.212 Angle : 0.677 13.622 13891 Z= 0.362 Chirality : 0.042 0.421 1619 Planarity : 0.005 0.051 1207 Dihedral : 24.578 167.186 3081 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 6.20 % Allowed : 25.43 % Favored : 68.37 % 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: -0.01 (0.31), residues: 736 helix: 1.77 (0.26), residues: 355 sheet: -1.34 (0.48), residues: 125 loop : -1.89 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 201 TYR 0.016 0.002 TYR A 348 PHE 0.017 0.002 PHE A 394 TRP 0.015 0.001 TRP A 51 HIS 0.006 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 ( 9762) covalent geometry : angle 0.66100 / 0.36 (13885) hydrogen bonds : bond 0.06033 / 3.93 ( 415) hydrogen bonds : angle 4.09573 / 2.97 ( 1109) metal coordination : bond 0.01165 / 0.53 ( 4) metal coordination : angle 7.08462 / 3.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 53 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6877 (m-10) REVERT: A 299 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8206 (mtm110) REVERT: A 314 ASP cc_start: 0.8549 (m-30) cc_final: 0.8300 (m-30) REVERT: A 371 ARG cc_start: 0.8941 (tpm170) cc_final: 0.8358 (tpt90) REVERT: A 372 HIS cc_start: 0.8780 (OUTLIER) cc_final: 0.8502 (t70) REVERT: B 16 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.6883 (p90) REVERT: B 26 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8169 (mpp) REVERT: B 201 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7753 (tmm160) REVERT: B 206 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7946 (tp) REVERT: B 306 HIS cc_start: 0.9645 (OUTLIER) cc_final: 0.9411 (t-90) REVERT: B 372 HIS cc_start: 0.7455 (t-90) cc_final: 0.7197 (t70) outliers start: 40 outliers final: 16 residues processed: 90 average time/residue: 0.0799 time to fit residues: 10.4816 Evaluate side-chains 75 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 174 HIS Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 372 HIS Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain B residue 16 TYR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 407 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.069237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.051418 restraints weight = 52380.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.053092 restraints weight = 25416.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.054120 restraints weight = 17083.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.054716 restraints weight = 13755.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.054891 restraints weight = 12257.325| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 9766 Z= 0.261 Angle : 0.724 14.961 13891 Z= 0.384 Chirality : 0.044 0.428 1619 Planarity : 0.005 0.052 1207 Dihedral : 24.643 168.700 3081 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.27 % Allowed : 26.20 % Favored : 68.53 % 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: -0.20 (0.31), residues: 736 helix: 1.44 (0.25), residues: 359 sheet: -1.16 (0.47), residues: 126 loop : -1.90 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 201 TYR 0.025 0.002 TYR B 199 PHE 0.013 0.002 PHE B 49 TRP 0.013 0.002 TRP A 51 HIS 0.006 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.26 ( 9762) covalent geometry : angle 0.70506 / 0.38 (13885) hydrogen bonds : bond 0.06225 / 4.09 ( 415) hydrogen bonds : angle 4.25217 / 3.10 ( 1109) metal coordination : bond 0.01481 / 0.65 ( 4) metal coordination : angle 8.01209 / 3.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 55 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8581 (mp) REVERT: A 299 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8336 (mtm110) REVERT: A 372 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.8466 (t70) REVERT: B 16 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7080 (p90) REVERT: B 26 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8429 (mpp) REVERT: B 206 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8037 (tp) REVERT: B 296 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.9224 (mtpt) REVERT: B 301 ARG cc_start: 0.9352 (OUTLIER) cc_final: 0.9055 (mtt180) REVERT: B 306 HIS cc_start: 0.9533 (OUTLIER) cc_final: 0.9256 (t-90) REVERT: B 372 HIS cc_start: 0.7285 (t-90) cc_final: 0.7080 (t-90) outliers start: 34 outliers final: 18 residues processed: 86 average time/residue: 0.0969 time to fit residues: 11.6548 Evaluate side-chains 79 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 372 HIS Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain B residue 16 TYR Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 306 HIS Chi-restraints excluded: chain B residue 407 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 46 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.0970 chunk 78 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 12 optimal weight: 0.3980 chunk 86 optimal weight: 9.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 ASN ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.071343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.054035 restraints weight = 52050.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.055771 restraints weight = 25162.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.056835 restraints weight = 16810.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.057337 restraints weight = 13439.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.057443 restraints weight = 12073.718| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9766 Z= 0.133 Angle : 0.630 12.679 13891 Z= 0.337 Chirality : 0.040 0.418 1619 Planarity : 0.005 0.048 1207 Dihedral : 24.579 172.010 3081 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.43 % Allowed : 27.75 % Favored : 66.82 % 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: 0.08 (0.31), residues: 736 helix: 1.74 (0.26), residues: 359 sheet: -1.10 (0.45), residues: 132 loop : -1.84 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 201 TYR 0.017 0.001 TYR B 199 PHE 0.020 0.001 PHE A 394 TRP 0.012 0.001 TRP A 51 HIS 0.005 0.001 HIS B 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 9762) covalent geometry : angle 0.61650 / 0.34 (13885) hydrogen bonds : bond 0.05647 / 3.61 ( 415) hydrogen bonds : angle 3.85643 / 2.79 ( 1109) metal coordination : bond 0.01029 / 0.49 ( 4) metal coordination : angle 6.23868 / 2.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 52 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8509 (mp) REVERT: A 210 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7348 (m-10) REVERT: A 299 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8288 (mtm110) REVERT: A 371 ARG cc_start: 0.8837 (tpm170) cc_final: 0.8306 (tpt90) REVERT: A 372 HIS cc_start: 0.8509 (OUTLIER) cc_final: 0.8245 (t70) REVERT: B 16 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.6803 (p90) REVERT: B 26 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8118 (mpp) REVERT: B 206 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7931 (tp) outliers start: 35 outliers final: 19 residues processed: 83 average time/residue: 0.0854 time to fit residues: 9.9496 Evaluate side-chains 76 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 135 LYS Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 372 HIS Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain B residue 16 TYR Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 407 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 15 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 29 GLN B 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.069752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.052168 restraints weight = 52258.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.053853 restraints weight = 25353.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.054892 restraints weight = 16978.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.055480 restraints weight = 13622.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.055804 restraints weight = 12126.095| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 9766 Z= 0.210 Angle : 0.667 13.579 13891 Z= 0.354 Chirality : 0.041 0.402 1619 Planarity : 0.005 0.057 1207 Dihedral : 24.503 168.410 3081 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.43 % Allowed : 27.44 % Favored : 67.13 % 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: 0.06 (0.31), residues: 736 helix: 1.67 (0.26), residues: 359 sheet: -1.11 (0.46), residues: 132 loop : -1.75 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.019 0.002 TYR B 199 PHE 0.010 0.001 PHE A 182 TRP 0.012 0.001 TRP A 51 HIS 0.005 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 ( 9762) covalent geometry : angle 0.65149 / 0.35 (13885) hydrogen bonds : bond 0.05688 / 3.67 ( 415) hydrogen bonds : angle 3.96140 / 2.87 ( 1109) metal coordination : bond 0.01133 / 0.52 ( 4) metal coordination : angle 7.00689 / 3.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 51 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 299 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8354 (mtm110) REVERT: B 16 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.6910 (p90) REVERT: B 26 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8099 (mpp) REVERT: B 154 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: B 206 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7955 (tp) outliers start: 35 outliers final: 20 residues processed: 82 average time/residue: 0.0792 time to fit residues: 9.2854 Evaluate side-chains 77 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain B residue 16 TYR Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 195 CYS Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 407 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.0470 chunk 27 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 10.9990 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 HIS B 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.070552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.053012 restraints weight = 51824.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.054710 restraints weight = 25367.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.055750 restraints weight = 17118.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.056355 restraints weight = 13807.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.056616 restraints weight = 12281.435| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9766 Z= 0.146 Angle : 0.636 14.816 13891 Z= 0.336 Chirality : 0.039 0.410 1619 Planarity : 0.005 0.052 1207 Dihedral : 24.477 171.320 3079 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.50 % Allowed : 28.84 % Favored : 66.67 % 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: 0.14 (0.31), residues: 736 helix: 1.74 (0.26), residues: 359 sheet: -1.01 (0.45), residues: 132 loop : -1.76 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.019 0.001 TYR B 199 PHE 0.023 0.001 PHE A 394 TRP 0.012 0.001 TRP A 51 HIS 0.003 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 ( 9762) covalent geometry : angle 0.61949 / 0.34 (13885) hydrogen bonds : bond 0.05473 / 3.49 ( 415) hydrogen bonds : angle 3.81838 / 2.76 ( 1109) metal coordination : bond 0.01277 / 0.56 ( 4) metal coordination : angle 6.97132 / 2.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 50 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8524 (mp) REVERT: A 299 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8297 (mtm110) REVERT: A 302 ASP cc_start: 0.9015 (t0) cc_final: 0.8593 (t0) REVERT: A 371 ARG cc_start: 0.8859 (tpm170) cc_final: 0.8395 (tpt90) REVERT: B 16 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.6937 (p90) REVERT: B 26 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8034 (mpp) REVERT: B 206 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7946 (tp) outliers start: 29 outliers final: 17 residues processed: 75 average time/residue: 0.0736 time to fit residues: 8.2272 Evaluate side-chains 71 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain B residue 16 TYR Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 407 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 62 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 22 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 HIS B 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.070855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.053390 restraints weight = 51584.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.055107 restraints weight = 25068.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.056172 restraints weight = 16778.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.056777 restraints weight = 13434.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.057083 restraints weight = 11920.835| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9766 Z= 0.138 Angle : 0.633 13.424 13891 Z= 0.333 Chirality : 0.039 0.407 1619 Planarity : 0.004 0.049 1207 Dihedral : 24.412 172.415 3079 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.03 % Allowed : 28.68 % Favored : 67.29 % 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: 0.19 (0.32), residues: 736 helix: 1.78 (0.26), residues: 360 sheet: -0.93 (0.46), residues: 132 loop : -1.81 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 117 TYR 0.021 0.001 TYR B 199 PHE 0.009 0.001 PHE A 49 TRP 0.009 0.001 TRP A 51 HIS 0.006 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 9762) covalent geometry : angle 0.61927 / 0.33 (13885) hydrogen bonds : bond 0.05358 / 3.39 ( 415) hydrogen bonds : angle 3.76936 / 2.73 ( 1109) metal coordination : bond 0.01056 / 0.49 ( 4) metal coordination : angle 6.30306 / 2.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8511 (mp) REVERT: A 210 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7996 (m-80) REVERT: A 299 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8286 (mtm110) REVERT: A 371 ARG cc_start: 0.8857 (tpm170) cc_final: 0.8390 (tpt90) REVERT: A 410 SER cc_start: 0.9323 (OUTLIER) cc_final: 0.8617 (t) REVERT: B 16 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.6911 (p90) REVERT: B 26 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8023 (mpp) REVERT: B 171 MET cc_start: 0.4598 (tpp) cc_final: 0.4300 (tpt) REVERT: B 206 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7974 (tp) outliers start: 26 outliers final: 16 residues processed: 73 average time/residue: 0.0885 time to fit residues: 9.2161 Evaluate side-chains 72 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 210 TYR Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain B residue 16 TYR Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 407 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 79 optimal weight: 30.0000 chunk 72 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN A 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.068958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.051193 restraints weight = 52468.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.052894 restraints weight = 25356.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.053945 restraints weight = 17022.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.054522 restraints weight = 13633.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.054815 restraints weight = 12164.558| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 9766 Z= 0.230 Angle : 0.702 16.211 13891 Z= 0.369 Chirality : 0.042 0.415 1619 Planarity : 0.005 0.045 1207 Dihedral : 24.438 168.477 3079 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.72 % Allowed : 28.37 % Favored : 67.91 % 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: -0.08 (0.31), residues: 736 helix: 1.51 (0.26), residues: 360 sheet: -1.15 (0.45), residues: 132 loop : -1.79 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 376 TYR 0.022 0.002 TYR B 199 PHE 0.021 0.002 PHE A 394 TRP 0.014 0.002 TRP A 51 HIS 0.006 0.002 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 ( 9762) covalent geometry : angle 0.68400 / 0.37 (13885) hydrogen bonds : bond 0.05833 / 3.77 ( 415) hydrogen bonds : angle 4.02524 / 2.92 ( 1109) metal coordination : bond 0.01442 / 0.64 ( 4) metal coordination : angle 7.66898 / 3.16 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8602 (mp) REVERT: A 299 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8300 (mtm110) REVERT: A 302 ASP cc_start: 0.9132 (t0) cc_final: 0.8742 (t0) REVERT: A 371 ARG cc_start: 0.8926 (tpm170) cc_final: 0.8421 (tpt90) REVERT: B 16 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.6859 (p90) REVERT: B 26 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8022 (mpp) REVERT: B 120 MET cc_start: 0.8860 (tpt) cc_final: 0.8624 (tpp) REVERT: B 206 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8022 (tp) REVERT: B 326 MET cc_start: 0.8435 (tmm) cc_final: 0.8087 (tmm) outliers start: 24 outliers final: 17 residues processed: 73 average time/residue: 0.0871 time to fit residues: 9.1779 Evaluate side-chains 73 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 273 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain B residue 16 TYR Chi-restraints excluded: chain B residue 26 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 407 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 61 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN B 80 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.069814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.052253 restraints weight = 51906.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.053946 restraints weight = 25346.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.055001 restraints weight = 17055.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.055570 restraints weight = 13680.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.055832 restraints weight = 12190.012| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9766 Z= 0.157 Angle : 0.647 14.363 13891 Z= 0.341 Chirality : 0.040 0.425 1619 Planarity : 0.004 0.044 1207 Dihedral : 24.446 172.100 3079 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.57 % Allowed : 29.30 % Favored : 67.13 % 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: 0.06 (0.31), residues: 736 helix: 1.67 (0.26), residues: 360 sheet: -1.04 (0.44), residues: 135 loop : -1.83 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 263 TYR 0.022 0.002 TYR B 199 PHE 0.016 0.001 PHE A 394 TRP 0.011 0.001 TRP A 51 HIS 0.004 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 ( 9762) covalent geometry : angle 0.63158 / 0.34 (13885) hydrogen bonds : bond 0.05434 / 3.45 ( 415) hydrogen bonds : angle 3.81920 / 2.77 ( 1109) metal coordination : bond 0.01116 / 0.51 ( 4) metal coordination : angle 6.73451 / 2.77 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1555.51 seconds wall clock time: 27 minutes 38.13 seconds (1658.13 seconds total)