Starting phenix.real_space_refine on Thu Jul 2 16:06:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lir_63121/07_2026/9lir_63121.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lir_63121/07_2026/9lir_63121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lir_63121/07_2026/9lir_63121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lir_63121/07_2026/9lir_63121.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lir_63121/07_2026/9lir_63121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lir_63121/07_2026/9lir_63121.map" } resolution = 3.1 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 247 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 4857 2.51 5 N 1713 2.21 5 O 2361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9208 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 4141 Classifications: {'RNA': 194} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 13, 'rna3p_pur': 90, 'rna3p_pyr': 77} Link IDs: {'rna2p': 27, 'rna3p': 166} Chain: "B" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 560 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 527 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3977 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7106 SG CYS D 234 15.817 50.167 51.455 1.00 55.62 S ATOM 7131 SG CYS D 237 13.004 50.297 49.029 1.00 48.00 S ATOM 7359 SG CYS D 265 16.628 49.971 47.565 1.00 32.21 S Time building chain proxies: 1.54, per 1000 atoms: 0.17 Number of scatterers: 9208 At special positions: 0 Unit cell: (103.416, 122.598, 110.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 27 16.00 P 247 15.00 Mg 2 11.99 O 2361 8.00 N 1713 7.00 C 4857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 348 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 154.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" ND1 HIS D 268 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 237 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 234 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 265 " Number of angles added : 3 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 922 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 6 sheets defined 32.0% alpha, 4.5% beta 57 base pairs and 130 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'D' and resid 20 through 26 Processing helix chain 'D' and resid 27 through 29 No H-bonds generated for 'chain 'D' and resid 27 through 29' Processing helix chain 'D' and resid 85 through 87 No H-bonds generated for 'chain 'D' and resid 85 through 87' Processing helix chain 'D' and resid 88 through 109 removed outlier: 4.381A pdb=" N LYS D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 163 through 184 Processing helix chain 'D' and resid 207 through 212 removed outlier: 4.119A pdb=" N GLN D 212 " --> pdb=" O TRP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 230 removed outlier: 3.687A pdb=" N SER D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 275 Processing helix chain 'D' and resid 278 through 284 Processing helix chain 'D' and resid 297 through 303 removed outlier: 3.513A pdb=" N GLN D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 314 removed outlier: 5.934A pdb=" N GLN D 309 " --> pdb=" O TYR D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 342 through 347 Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 444 through 449 Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 7 removed outlier: 4.095A pdb=" N VAL D 6 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.794A pdb=" N GLY D 67 " --> pdb=" O ASP D 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 129 through 131 removed outlier: 3.579A pdb=" N ARG D 131 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 189 through 190 removed outlier: 7.361A pdb=" N VAL D 189 " --> pdb=" O CYS D 319 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 243 through 246 Processing sheet with id=AA6, first strand: chain 'D' and resid 469 through 470 103 hydrogen bonds defined for protein. 279 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 151 hydrogen bonds 282 hydrogen bond angles 0 basepair planarities 57 basepair parallelities 130 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1404 1.33 - 1.45: 3840 1.45 - 1.57: 4132 1.57 - 1.69: 491 1.69 - 1.81: 42 Bond restraints: 9909 Sorted by residual: bond pdb=" C3' DG B 10 " pdb=" C2' DG B 10 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.35e+01 bond pdb=" C3' DA C 13 " pdb=" C2' DA C 13 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DA B 8 " pdb=" C2' DA B 8 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DA B 26 " pdb=" O3' DA B 26 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" N1 U A 94 " pdb=" C2 U A 94 " ideal model delta sigma weight residual 1.381 1.410 -0.029 9.00e-03 1.23e+04 1.02e+01 ... (remaining 9904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 14368 3.00 - 6.01: 154 6.01 - 9.01: 21 9.01 - 12.02: 1 12.02 - 15.02: 1 Bond angle restraints: 14545 Sorted by residual: angle pdb=" N1 U A 94 " pdb=" C2 U A 94 " pdb=" O2 U A 94 " ideal model delta sigma weight residual 122.80 129.43 -6.63 7.00e-01 2.04e+00 8.97e+01 angle pdb=" C1' U A 94 " pdb=" N1 U A 94 " pdb=" C2 U A 94 " ideal model delta sigma weight residual 117.70 128.43 -10.73 1.20e+00 6.94e-01 8.00e+01 angle pdb=" O2 U A 94 " pdb=" C2 U A 94 " pdb=" N3 U A 94 " ideal model delta sigma weight residual 122.20 116.02 6.18 7.00e-01 2.04e+00 7.79e+01 angle pdb=" C5 G A 136 " pdb=" C4 G A 136 " pdb=" N3 G A 136 " ideal model delta sigma weight residual 128.60 125.50 3.10 5.00e-01 4.00e+00 3.83e+01 angle pdb=" N9 G A 136 " pdb=" C4 G A 136 " pdb=" N3 G A 136 " ideal model delta sigma weight residual 126.00 129.71 -3.71 6.00e-01 2.78e+00 3.82e+01 ... (remaining 14540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 5187 35.26 - 70.52: 803 70.52 - 105.78: 86 105.78 - 141.04: 2 141.04 - 176.30: 10 Dihedral angle restraints: 6088 sinusoidal: 4653 harmonic: 1435 Sorted by residual: dihedral pdb=" O4' C A 80 " pdb=" C1' C A 80 " pdb=" N1 C A 80 " pdb=" C2 C A 80 " ideal model delta sinusoidal sigma weight residual 200.00 42.88 157.12 1 1.50e+01 4.44e-03 8.20e+01 dihedral pdb=" O4' U A 190 " pdb=" C1' U A 190 " pdb=" N1 U A 190 " pdb=" C2 U A 190 " ideal model delta sinusoidal sigma weight residual 200.00 48.74 151.26 1 1.50e+01 4.44e-03 8.01e+01 dihedral pdb=" O4' U A 166 " pdb=" C1' U A 166 " pdb=" N1 U A 166 " pdb=" C2 U A 166 " ideal model delta sinusoidal sigma weight residual 232.00 55.70 176.30 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 6085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1433 0.049 - 0.099: 244 0.099 - 0.148: 64 0.148 - 0.197: 13 0.197 - 0.246: 5 Chirality restraints: 1759 Sorted by residual: chirality pdb=" C3' A A 83 " pdb=" C4' A A 83 " pdb=" O3' A A 83 " pdb=" C2' A A 83 " both_signs ideal model delta sigma weight residual False -2.48 -2.23 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C1' U A 7 " pdb=" O4' U A 7 " pdb=" C2' U A 7 " pdb=" N1 U A 7 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C2' G A 30 " pdb=" C3' G A 30 " pdb=" O2' G A 30 " pdb=" C1' G A 30 " both_signs ideal model delta sigma weight residual False -2.52 -2.31 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1756 not shown) Planarity restraints: 953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 106 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.48e+00 pdb=" C ARG D 106 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG D 106 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU D 107 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 2 " -0.031 2.00e-02 2.50e+03 1.56e-02 5.49e+00 pdb=" N1 C A 2 " 0.033 2.00e-02 2.50e+03 pdb=" C2 C A 2 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C A 2 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C A 2 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C A 2 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C A 2 " -0.009 2.00e-02 2.50e+03 pdb=" C5 C A 2 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C A 2 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 163 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO D 164 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " 0.030 5.00e-02 4.00e+02 ... (remaining 950 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 137 2.64 - 3.20: 7687 3.20 - 3.77: 18715 3.77 - 4.33: 23608 4.33 - 4.90: 32258 Nonbonded interactions: 82405 Sorted by model distance: nonbonded pdb=" OP2 DC C 22 " pdb="MG MG C 101 " model vdw 2.071 2.170 nonbonded pdb=" OD2 ASP D 60 " pdb="MG MG C 101 " model vdw 2.087 2.170 nonbonded pdb=" NE2 HIS D 269 " pdb="MG MG D 601 " model vdw 2.205 2.250 nonbonded pdb=" O2 U A 62 " pdb=" N2 G A 117 " model vdw 2.295 2.496 nonbonded pdb=" NE2 HIS D 273 " pdb="MG MG D 601 " model vdw 2.308 2.250 ... (remaining 82400 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: 1.440 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.250 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9914 Z= 0.342 Angle : 0.857 15.019 14550 Z= 0.714 Chirality : 0.044 0.246 1759 Planarity : 0.006 0.054 953 Dihedral : 26.301 176.302 5163 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.18 % Favored : 88.62 % Rotamer: Outliers : 4.21 % Allowed : 30.61 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.34), residues: 492 helix: -2.34 (0.38), residues: 137 sheet: -1.98 (1.30), residues: 17 loop : -2.52 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 151 TYR 0.011 0.001 TYR D 340 PHE 0.031 0.003 PHE D 469 TRP 0.021 0.002 TRP D 161 HIS 0.008 0.001 HIS D 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.34 ( 9909) covalent geometry : angle 0.85456 / 0.71 (14545) SS BOND : bond 0.01042 / 0.52 ( 1) SS BOND : angle 0.38112 / 0.64 ( 2) hydrogen bonds : bond 0.12961 / 11.04 ( 254) hydrogen bonds : angle 7.30114 / 9.94 ( 561) metal coordination : bond 0.01187 / 0.79 ( 4) metal coordination : angle 4.71278 / 5.84 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 23 time to evaluate : 0.174 Fit side-chains REVERT: D 216 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9107 (pp) REVERT: D 449 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8722 (pp20) outliers start: 18 outliers final: 11 residues processed: 41 average time/residue: 0.1095 time to fit residues: 6.0032 Evaluate side-chains 32 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 427 LYS Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 470 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.057280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.055708 restraints weight = 38596.435| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 0.73 r_work: 0.2803 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9914 Z= 0.134 Angle : 0.591 12.274 14550 Z= 0.346 Chirality : 0.038 0.252 1759 Planarity : 0.004 0.045 953 Dihedral : 26.924 178.560 4168 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.98 % Favored : 88.82 % Rotamer: Outliers : 5.37 % Allowed : 29.21 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.28 (0.35), residues: 492 helix: -2.05 (0.39), residues: 141 sheet: -1.78 (1.10), residues: 23 loop : -2.40 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 151 TYR 0.010 0.001 TYR D 340 PHE 0.019 0.001 PHE D 453 TRP 0.012 0.001 TRP D 161 HIS 0.002 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.13 ( 9909) covalent geometry : angle 0.58950 / 0.35 (14545) SS BOND : bond 0.00602 / 0.30 ( 1) SS BOND : angle 0.58000 / 0.87 ( 2) hydrogen bonds : bond 0.08037 / 8.33 ( 254) hydrogen bonds : angle 5.32537 / 5.57 ( 561) metal coordination : bond 0.01054 / 0.68 ( 4) metal coordination : angle 3.18850 / 3.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 20 time to evaluate : 0.259 Fit side-chains REVERT: D 216 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9095 (pp) REVERT: D 449 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.7270 (pp20) REVERT: D 473 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.6556 (tt0) outliers start: 23 outliers final: 10 residues processed: 41 average time/residue: 0.0821 time to fit residues: 4.9444 Evaluate side-chains 32 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 427 LYS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 482 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.048510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.047108 restraints weight = 40255.924| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 0.69 r_work: 0.2572 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9914 Z= 0.277 Angle : 0.715 13.691 14550 Z= 0.403 Chirality : 0.044 0.210 1759 Planarity : 0.006 0.046 953 Dihedral : 27.019 179.297 4157 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.62 % Favored : 86.18 % Rotamer: Outliers : 5.84 % Allowed : 30.61 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.36), residues: 492 helix: -1.87 (0.40), residues: 134 sheet: -2.41 (0.93), residues: 33 loop : -2.40 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 113 TYR 0.013 0.002 TYR D 340 PHE 0.017 0.002 PHE D 453 TRP 0.013 0.002 TRP D 161 HIS 0.007 0.002 HIS D 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.28 ( 9909) covalent geometry : angle 0.70518 / 0.40 (14545) SS BOND : bond 0.00106 / 0.05 ( 1) SS BOND : angle 0.71732 / 0.84 ( 2) hydrogen bonds : bond 0.08670 / 8.93 ( 254) hydrogen bonds : angle 5.51414 / 5.46 ( 561) metal coordination : bond 0.03154 / 1.96 ( 4) metal coordination : angle 8.14165 / 6.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 21 time to evaluate : 0.213 Fit side-chains REVERT: D 286 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.7867 (tptt) REVERT: D 473 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.7025 (tt0) outliers start: 25 outliers final: 13 residues processed: 43 average time/residue: 0.0806 time to fit residues: 5.1409 Evaluate side-chains 33 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 18 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 482 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 175 ASN ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.050535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.049064 restraints weight = 39297.603| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 0.67 r_work: 0.2629 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9914 Z= 0.164 Angle : 0.607 12.041 14550 Z= 0.353 Chirality : 0.039 0.197 1759 Planarity : 0.004 0.044 953 Dihedral : 27.091 176.408 4146 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.59 % Favored : 88.21 % Rotamer: Outliers : 6.54 % Allowed : 30.84 % Favored : 62.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.36), residues: 492 helix: -1.73 (0.41), residues: 128 sheet: -1.66 (1.14), residues: 23 loop : -2.27 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 109 TYR 0.012 0.001 TYR D 305 PHE 0.015 0.002 PHE D 453 TRP 0.009 0.001 TRP D 161 HIS 0.003 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 ( 9909) covalent geometry : angle 0.60354 / 0.35 (14545) SS BOND : bond 0.00425 / 0.21 ( 1) SS BOND : angle 0.74841 / 1.08 ( 2) hydrogen bonds : bond 0.07705 / 8.14 ( 254) hydrogen bonds : angle 5.42185 / 5.35 ( 561) metal coordination : bond 0.01595 / 1.00 ( 4) metal coordination : angle 4.22938 / 4.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 18 time to evaluate : 0.213 Fit side-chains REVERT: D 267 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.7444 (pm20) REVERT: D 286 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8028 (tptt) REVERT: D 473 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.7073 (tt0) outliers start: 28 outliers final: 20 residues processed: 43 average time/residue: 0.0867 time to fit residues: 5.4443 Evaluate side-chains 41 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 18 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 211 TYR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 340 TYR Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 427 LYS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.048687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.047278 restraints weight = 39852.213| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 0.68 r_work: 0.2575 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9914 Z= 0.234 Angle : 0.650 12.158 14550 Z= 0.373 Chirality : 0.042 0.200 1759 Planarity : 0.005 0.045 953 Dihedral : 27.063 179.906 4146 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.62 % Favored : 86.18 % Rotamer: Outliers : 6.54 % Allowed : 31.07 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.36), residues: 492 helix: -1.86 (0.40), residues: 134 sheet: -1.74 (1.16), residues: 23 loop : -2.29 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 113 TYR 0.012 0.002 TYR D 340 PHE 0.013 0.002 PHE D 453 TRP 0.010 0.001 TRP D 161 HIS 0.004 0.001 HIS D 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.23 ( 9909) covalent geometry : angle 0.64569 / 0.37 (14545) SS BOND : bond 0.00175 / 0.09 ( 1) SS BOND : angle 0.77314 / 0.92 ( 2) hydrogen bonds : bond 0.08316 / 8.66 ( 254) hydrogen bonds : angle 5.48422 / 5.39 ( 561) metal coordination : bond 0.02562 / 1.60 ( 4) metal coordination : angle 5.00872 / 4.94 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 18 time to evaluate : 0.190 Fit side-chains REVERT: D 267 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.7444 (pm20) REVERT: D 286 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.7949 (tptt) REVERT: D 473 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.7077 (tt0) outliers start: 28 outliers final: 21 residues processed: 43 average time/residue: 0.0864 time to fit residues: 5.2677 Evaluate side-chains 42 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 18 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 211 TYR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 340 TYR Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 427 LYS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.049841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.048406 restraints weight = 39346.352| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 0.68 r_work: 0.2608 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9914 Z= 0.172 Angle : 0.605 12.281 14550 Z= 0.352 Chirality : 0.039 0.200 1759 Planarity : 0.004 0.044 953 Dihedral : 27.101 177.969 4146 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.60 % Favored : 87.20 % Rotamer: Outliers : 7.24 % Allowed : 31.78 % Favored : 60.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.36), residues: 492 helix: -1.75 (0.41), residues: 128 sheet: -1.77 (1.15), residues: 23 loop : -2.25 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 486 TYR 0.011 0.001 TYR D 305 PHE 0.013 0.002 PHE D 453 TRP 0.012 0.001 TRP D 161 HIS 0.002 0.001 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.17 ( 9909) covalent geometry : angle 0.60281 / 0.35 (14545) SS BOND : bond 0.00371 / 0.19 ( 1) SS BOND : angle 0.73711 / 1.06 ( 2) hydrogen bonds : bond 0.07805 / 8.26 ( 254) hydrogen bonds : angle 5.43168 / 5.32 ( 561) metal coordination : bond 0.01478 / 0.89 ( 4) metal coordination : angle 3.54088 / 4.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 18 time to evaluate : 0.150 Fit side-chains REVERT: D 223 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.8736 (mt-10) REVERT: D 267 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.7442 (pm20) REVERT: D 286 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8016 (tptt) REVERT: D 473 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.7108 (tt0) outliers start: 31 outliers final: 24 residues processed: 47 average time/residue: 0.0855 time to fit residues: 5.5992 Evaluate side-chains 46 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 18 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 211 TYR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 340 TYR Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 427 LYS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 19 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.052535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.051039 restraints weight = 39194.753| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 0.68 r_work: 0.2685 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9914 Z= 0.132 Angle : 0.573 12.413 14550 Z= 0.336 Chirality : 0.038 0.207 1759 Planarity : 0.004 0.042 953 Dihedral : 27.085 174.400 4146 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.20 % Favored : 87.60 % Rotamer: Outliers : 6.54 % Allowed : 33.18 % Favored : 60.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.36), residues: 492 helix: -1.80 (0.40), residues: 134 sheet: -1.73 (1.13), residues: 23 loop : -2.29 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 19 TYR 0.012 0.001 TYR D 305 PHE 0.015 0.002 PHE D 453 TRP 0.013 0.001 TRP D 161 HIS 0.002 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 ( 9909) covalent geometry : angle 0.57181 / 0.34 (14545) SS BOND : bond 0.00457 / 0.23 ( 1) SS BOND : angle 0.81578 / 1.36 ( 2) hydrogen bonds : bond 0.07257 / 7.80 ( 254) hydrogen bonds : angle 5.26497 / 5.13 ( 561) metal coordination : bond 0.00523 / 0.27 ( 4) metal coordination : angle 2.57541 / 3.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 18 time to evaluate : 0.233 Fit side-chains REVERT: D 216 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9165 (pp) REVERT: D 267 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.7477 (pm20) REVERT: D 286 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8012 (tptt) REVERT: D 473 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.7041 (tt0) outliers start: 28 outliers final: 20 residues processed: 44 average time/residue: 0.0738 time to fit residues: 4.7826 Evaluate side-chains 42 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 18 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 211 TYR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 427 LYS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 21 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.051363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.049927 restraints weight = 38273.912| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 0.66 r_work: 0.2653 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9914 Z= 0.163 Angle : 0.588 12.151 14550 Z= 0.341 Chirality : 0.038 0.199 1759 Planarity : 0.004 0.042 953 Dihedral : 27.037 174.853 4146 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.80 % Favored : 86.99 % Rotamer: Outliers : 6.31 % Allowed : 33.18 % Favored : 60.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.91 (0.36), residues: 492 helix: -1.66 (0.41), residues: 128 sheet: -1.87 (1.12), residues: 23 loop : -2.18 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 84 TYR 0.010 0.001 TYR D 340 PHE 0.014 0.001 PHE D 453 TRP 0.012 0.001 TRP D 161 HIS 0.002 0.001 HIS D 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 ( 9909) covalent geometry : angle 0.58593 / 0.34 (14545) SS BOND : bond 0.00352 / 0.18 ( 1) SS BOND : angle 0.64545 / 1.02 ( 2) hydrogen bonds : bond 0.07470 / 7.99 ( 254) hydrogen bonds : angle 5.25740 / 5.12 ( 561) metal coordination : bond 0.01385 / 0.82 ( 4) metal coordination : angle 3.20798 / 4.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 18 time to evaluate : 0.171 Fit side-chains REVERT: D 216 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9172 (pp) REVERT: D 267 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.7458 (pm20) REVERT: D 286 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.7981 (tptt) REVERT: D 449 GLU cc_start: 0.9380 (OUTLIER) cc_final: 0.7735 (pp20) REVERT: D 473 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7054 (tt0) outliers start: 27 outliers final: 19 residues processed: 43 average time/residue: 0.0911 time to fit residues: 5.5907 Evaluate side-chains 42 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 18 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 211 TYR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 427 LYS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 449 GLU Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.049873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.048446 restraints weight = 39008.001| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 0.67 r_work: 0.2609 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9914 Z= 0.193 Angle : 0.612 12.097 14550 Z= 0.354 Chirality : 0.040 0.192 1759 Planarity : 0.004 0.042 953 Dihedral : 27.053 177.547 4146 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.21 % Favored : 86.59 % Rotamer: Outliers : 6.07 % Allowed : 33.88 % Favored : 60.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.94 (0.36), residues: 492 helix: -1.66 (0.42), residues: 128 sheet: -1.84 (1.13), residues: 23 loop : -2.22 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 113 TYR 0.011 0.001 TYR D 340 PHE 0.013 0.002 PHE D 453 TRP 0.010 0.001 TRP D 161 HIS 0.003 0.001 HIS D 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.19 ( 9909) covalent geometry : angle 0.61014 / 0.35 (14545) SS BOND : bond 0.00304 / 0.15 ( 1) SS BOND : angle 0.64987 / 0.87 ( 2) hydrogen bonds : bond 0.07812 / 8.31 ( 254) hydrogen bonds : angle 5.35154 / 5.21 ( 561) metal coordination : bond 0.02026 / 1.25 ( 4) metal coordination : angle 3.60102 / 4.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 18 time to evaluate : 0.229 Fit side-chains REVERT: D 267 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: D 286 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8025 (tptt) REVERT: D 473 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.7092 (tt0) outliers start: 26 outliers final: 21 residues processed: 42 average time/residue: 0.0736 time to fit residues: 4.4374 Evaluate side-chains 42 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 18 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 211 TYR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 427 LYS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 46 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.049554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.048126 restraints weight = 39646.945| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 0.67 r_work: 0.2600 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9914 Z= 0.198 Angle : 0.616 12.257 14550 Z= 0.356 Chirality : 0.040 0.194 1759 Planarity : 0.004 0.042 953 Dihedral : 27.066 178.261 4146 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.01 % Favored : 86.79 % Rotamer: Outliers : 6.54 % Allowed : 33.64 % Favored : 59.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.36), residues: 492 helix: -1.73 (0.41), residues: 128 sheet: -1.85 (1.15), residues: 23 loop : -2.25 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 113 TYR 0.011 0.001 TYR D 340 PHE 0.013 0.002 PHE D 453 TRP 0.010 0.001 TRP D 161 HIS 0.003 0.001 HIS D 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.20 ( 9909) covalent geometry : angle 0.61449 / 0.36 (14545) SS BOND : bond 0.00275 / 0.14 ( 1) SS BOND : angle 0.72191 / 0.95 ( 2) hydrogen bonds : bond 0.07886 / 8.36 ( 254) hydrogen bonds : angle 5.41473 / 5.27 ( 561) metal coordination : bond 0.02064 / 1.27 ( 4) metal coordination : angle 3.44337 / 4.00 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 18 time to evaluate : 0.212 Fit side-chains REVERT: D 223 GLU cc_start: 0.9346 (OUTLIER) cc_final: 0.8782 (mt-10) REVERT: D 267 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.7434 (pm20) REVERT: D 286 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8029 (tptt) REVERT: D 473 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.7119 (tt0) outliers start: 28 outliers final: 23 residues processed: 44 average time/residue: 0.0943 time to fit residues: 5.9023 Evaluate side-chains 45 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 18 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 211 TYR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 266 GLU Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 340 TYR Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 382 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 427 LYS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 473 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 69 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.049850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.048423 restraints weight = 38847.715| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 0.67 r_work: 0.2609 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9914 Z= 0.170 Angle : 0.605 12.255 14550 Z= 0.351 Chirality : 0.039 0.197 1759 Planarity : 0.004 0.042 953 Dihedral : 27.082 177.904 4146 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.80 % Favored : 86.99 % Rotamer: Outliers : 6.07 % Allowed : 34.11 % Favored : 59.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.98 (0.36), residues: 492 helix: -1.70 (0.41), residues: 128 sheet: -1.94 (1.13), residues: 23 loop : -2.23 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 157 TYR 0.011 0.001 TYR D 305 PHE 0.014 0.002 PHE D 453 TRP 0.011 0.001 TRP D 161 HIS 0.003 0.001 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 ( 9909) covalent geometry : angle 0.60390 / 0.35 (14545) SS BOND : bond 0.00321 / 0.16 ( 1) SS BOND : angle 0.71726 / 1.01 ( 2) hydrogen bonds : bond 0.07770 / 8.26 ( 254) hydrogen bonds : angle 5.40455 / 5.25 ( 561) metal coordination : bond 0.01606 / 0.97 ( 4) metal coordination : angle 2.94910 / 3.79 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1516.98 seconds wall clock time: 26 minutes 57.82 seconds (1617.82 seconds total)