Starting phenix.real_space_refine on Wed Aug 5 09:06:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lir_63121/08_2026/9lir_63121.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lir_63121/08_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_63121/08_2026/9lir_63121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lir_63121/08_2026/9lir_63121.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lir_63121/08_2026/9lir_63121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lir_63121/08_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-2.2rc3-6140/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: 2.12, per 1000 atoms: 0.23 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: 0.75 Conformation dependent library (CDL) restraints added in 156.7 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: 1.36 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: 1.90 Time building geometry restraints manager: 0.99 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: 14347 3.00 - 6.01: 175 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=" O4' G A 30 " pdb=" C1' G A 30 " pdb=" N9 G A 30 " ideal model delta sigma weight residual 108.20 113.30 -5.10 8.00e-01 1.56e+00 4.07e+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 ... (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 - 0.057: 1300 0.057 - 0.115: 242 0.115 - 0.172: 207 0.172 - 0.230: 7 0.230 - 0.287: 3 Chirality restraints: 1759 Sorted by residual: 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 -2.60 -2.31 -0.29 2.00e-01 2.50e+01 2.06e+00 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 0.24 2.00e-01 2.50e+01 1.39e+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: 1.080 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.450 Find NCS groups from input model: 0.040 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.180 ------------------------------------------------------------------------------- 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= 0.354 Angle : 0.976 15.019 14550 Z= 0.814 Chirality : 0.061 0.287 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 0.00408 / 0.35 ( 9909) covalent geometry : angle 0.97410 / 0.81 (14545) SS BOND : bond 0.01042 / 0.52 ( 1) SS BOND : angle 0.38112 / 0.64 ( 2) hydrogen bonds : bond 0.12961 / 12.80 ( 254) hydrogen bonds : angle 7.30114 / 10.24 ( 561) metal coordination : bond 0.01187 / 0.99 ( 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 : 0.134 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: 0.7512 (pp20) outliers start: 18 outliers final: 11 residues processed: 41 average time/residue: 0.1079 time to fit residues: 6.0179 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 : 0.214 ------------------------------------------------------------------------------- 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 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 = 0.2881 r_free = 0.2881 target = 0.057276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.055709 restraints weight = 38658.020| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 0.74 r_work: 0.2803 rms_B_bonded: 1.26 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: 0.8654 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9914 Z= 0.135 Angle : 0.618 12.301 14550 Z= 0.353 Chirality : 0.041 0.447 1759 Planarity : 0.004 0.045 953 Dihedral : 26.853 178.954 4168 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 16.24 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: -3.11 (0.35), residues: 492 helix: -1.92 (0.40), residues: 135 sheet: -1.75 (1.11), residues: 23 loop : -2.29 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 270 TYR 0.010 0.001 TYR D 340 PHE 0.018 0.001 PHE D 453 TRP 0.013 0.001 TRP D 161 HIS 0.002 0.001 HIS D 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.13 ( 9909) covalent geometry : angle 0.61649 / 0.35 (14545) SS BOND : bond 0.00549 / 0.27 ( 1) SS BOND : angle 0.63388 / 0.98 ( 2) hydrogen bonds : bond 0.08367 / 9.21 ( 254) hydrogen bonds : angle 5.32752 / 5.97 ( 561) metal coordination : bond 0.01053 / 0.70 ( 4) metal coordination : angle 3.23216 / 3.78 ( 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 : 0.209 Fit side-chains REVERT: D 216 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9103 (pp) REVERT: D 449 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.7316 (pp20) REVERT: D 473 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.6543 (tt0) outliers start: 23 outliers final: 11 residues processed: 41 average time/residue: 0.0990 time to fit residues: 5.8858 Evaluate side-chains 33 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 19 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 239 HIS 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: 7.9990 chunk 46 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.2736 r_free = 0.2736 target = 0.051563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.050111 restraints weight = 39124.076| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 0.68 r_work: 0.2659 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9914 Z= 0.178 Angle : 0.660 11.718 14550 Z= 0.365 Chirality : 0.043 0.465 1759 Planarity : 0.005 0.044 953 Dihedral : 26.930 179.643 4157 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.80 % Favored : 86.99 % Rotamer: Outliers : 6.31 % Allowed : 29.91 % Favored : 63.79 % 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: -2.97 (0.36), residues: 492 helix: -1.65 (0.42), residues: 128 sheet: -1.53 (1.15), residues: 23 loop : -2.28 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 113 TYR 0.011 0.001 TYR D 340 PHE 0.018 0.002 PHE D 453 TRP 0.012 0.001 TRP D 161 HIS 0.005 0.001 HIS D 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.18 ( 9909) covalent geometry : angle 0.65478 / 0.36 (14545) SS BOND : bond 0.00320 / 0.16 ( 1) SS BOND : angle 0.50417 / 0.78 ( 2) hydrogen bonds : bond 0.08030 / 8.95 ( 254) hydrogen bonds : angle 5.25645 / 5.52 ( 561) metal coordination : bond 0.02169 / 1.29 ( 4) metal coordination : angle 5.74476 / 5.97 ( 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 47 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 20 time to evaluate : 0.227 Fit side-chains REVERT: D 286 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.7929 (tptt) REVERT: D 473 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.6941 (tt0) outliers start: 27 outliers final: 14 residues processed: 44 average time/residue: 0.0918 time to fit residues: 5.9199 Evaluate side-chains 35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 19 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 262 VAL 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 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: 4.9990 chunk 33 optimal weight: 9.9990 chunk 31 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 26 optimal weight: 0.3980 chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 overall best weight: 2.5784 ------------------------------------------------------------------------------- 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 = 0.2735 r_free = 0.2735 target = 0.051525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.050062 restraints weight = 39204.621| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 0.68 r_work: 0.2656 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9914 Z= 0.167 Angle : 0.625 12.164 14550 Z= 0.350 Chirality : 0.042 0.469 1759 Planarity : 0.004 0.042 953 Dihedral : 26.953 179.635 4146 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.99 % Favored : 87.80 % Rotamer: Outliers : 6.54 % Allowed : 30.61 % Favored : 62.85 % 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: -2.95 (0.36), residues: 492 helix: -1.68 (0.42), residues: 128 sheet: -1.63 (1.12), residues: 23 loop : -2.24 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 151 TYR 0.009 0.001 TYR D 340 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 0.00295 / 0.17 ( 9909) covalent geometry : angle 0.62256 / 0.35 (14545) SS BOND : bond 0.00354 / 0.18 ( 1) SS BOND : angle 0.70534 / 1.06 ( 2) hydrogen bonds : bond 0.07843 / 8.77 ( 254) hydrogen bonds : angle 5.29219 / 5.55 ( 561) metal coordination : bond 0.01655 / 0.99 ( 4) metal coordination : angle 4.02262 / 4.60 ( 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 : 0.230 Fit side-chains REVERT: D 267 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: D 286 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.7992 (tptt) REVERT: D 473 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7001 (tt0) outliers start: 28 outliers final: 20 residues processed: 44 average time/residue: 0.1006 time to fit residues: 6.3685 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 : 0.207 ------------------------------------------------------------------------------- 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 71 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 162 LEU 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 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 Chi-restraints excluded: chain D residue 482 CYS 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: 7.9990 chunk 69 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.2761 r_free = 0.2761 target = 0.052477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.050992 restraints weight = 38847.601| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 0.68 r_work: 0.2683 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9914 Z= 0.136 Angle : 0.599 12.422 14550 Z= 0.338 Chirality : 0.040 0.467 1759 Planarity : 0.004 0.040 953 Dihedral : 26.966 179.452 4146 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.18 % Favored : 88.62 % Rotamer: Outliers : 7.24 % Allowed : 29.67 % Favored : 63.08 % 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: -2.86 (0.36), residues: 492 helix: -1.59 (0.42), residues: 128 sheet: -1.67 (1.10), residues: 23 loop : -2.17 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 270 TYR 0.010 0.001 TYR D 340 PHE 0.013 0.001 PHE D 453 TRP 0.013 0.001 TRP D 161 HIS 0.002 0.001 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 ( 9909) covalent geometry : angle 0.59789 / 0.34 (14545) SS BOND : bond 0.00406 / 0.20 ( 1) SS BOND : angle 0.68416 / 1.10 ( 2) hydrogen bonds : bond 0.07653 / 8.60 ( 254) hydrogen bonds : angle 5.23395 / 5.47 ( 561) metal coordination : bond 0.00976 / 0.55 ( 4) metal coordination : angle 2.77401 / 4.15 ( 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 50 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 19 time to evaluate : 0.273 Fit side-chains REVERT: D 267 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: D 286 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.7929 (tptt) REVERT: D 473 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7004 (tt0) outliers start: 31 outliers final: 22 residues processed: 46 average time/residue: 0.0988 time to fit residues: 6.6034 Evaluate side-chains 44 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 19 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 162 LEU 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 366 MET 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 470 VAL Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 482 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 0.0050 chunk 57 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 overall best weight: 1.8998 ------------------------------------------------------------------------------- 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 = 0.2755 r_free = 0.2755 target = 0.052264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.050795 restraints weight = 38191.592| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 0.67 r_work: 0.2678 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9914 Z= 0.147 Angle : 0.604 12.357 14550 Z= 0.339 Chirality : 0.041 0.472 1759 Planarity : 0.004 0.041 953 Dihedral : 26.946 179.613 4146 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.20 % Favored : 87.60 % Rotamer: Outliers : 7.94 % Allowed : 29.67 % 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: -2.85 (0.36), residues: 492 helix: -1.57 (0.42), residues: 128 sheet: -1.69 (1.10), residues: 23 loop : -2.17 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 270 TYR 0.010 0.001 TYR D 340 PHE 0.014 0.001 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 0.00252 / 0.15 ( 9909) covalent geometry : angle 0.60238 / 0.34 (14545) SS BOND : bond 0.00354 / 0.18 ( 1) SS BOND : angle 0.62496 / 1.00 ( 2) hydrogen bonds : bond 0.07650 / 8.58 ( 254) hydrogen bonds : angle 5.20385 / 5.42 ( 561) metal coordination : bond 0.01201 / 0.69 ( 4) metal coordination : angle 3.00728 / 3.98 ( 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 53 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 19 time to evaluate : 0.226 Fit side-chains REVERT: D 216 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9168 (pp) REVERT: D 267 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.7385 (pm20) REVERT: D 286 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.7940 (tptt) REVERT: D 449 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.7285 (pp20) REVERT: D 473 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.6993 (tt0) outliers start: 34 outliers final: 20 residues processed: 49 average time/residue: 0.1023 time to fit residues: 7.1477 Evaluate side-chains 44 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 19 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 449 GLU 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 Chi-restraints excluded: chain D residue 482 CYS 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: 7.9990 chunk 31 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 overall best weight: 3.0086 ------------------------------------------------------------------------------- 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 = 0.2709 r_free = 0.2709 target = 0.050640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.049201 restraints weight = 38778.677| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 0.66 r_work: 0.2632 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9914 Z= 0.185 Angle : 0.637 12.367 14550 Z= 0.354 Chirality : 0.043 0.481 1759 Planarity : 0.004 0.042 953 Dihedral : 26.947 177.424 4146 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.01 % Favored : 86.79 % Rotamer: Outliers : 7.48 % Allowed : 30.37 % Favored : 62.15 % 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: -2.92 (0.36), residues: 492 helix: -1.62 (0.41), residues: 128 sheet: -1.74 (1.11), 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 0.012 0.002 TYR D 340 PHE 0.013 0.002 PHE D 453 TRP 0.007 0.001 TRP D 161 HIS 0.003 0.001 HIS D 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.18 ( 9909) covalent geometry : angle 0.63467 / 0.35 (14545) SS BOND : bond 0.00283 / 0.14 ( 1) SS BOND : angle 0.57875 / 0.78 ( 2) hydrogen bonds : bond 0.08017 / 8.95 ( 254) hydrogen bonds : angle 5.29134 / 5.50 ( 561) metal coordination : bond 0.01905 / 1.13 ( 4) metal coordination : angle 3.56779 / 4.11 ( 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 50 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 18 time to evaluate : 0.224 Fit side-chains REVERT: D 267 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.7385 (pm20) REVERT: D 286 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8002 (tptt) REVERT: D 449 GLU cc_start: 0.9348 (OUTLIER) cc_final: 0.7705 (pp20) REVERT: D 473 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.7066 (tt0) outliers start: 32 outliers final: 24 residues processed: 48 average time/residue: 0.1037 time to fit residues: 7.0710 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 : 0.282 ------------------------------------------------------------------------------- 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 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 345 CYS Chi-restraints excluded: chain D residue 382 ASN 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 449 GLU 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 Chi-restraints excluded: chain D residue 482 CYS 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: 3.9990 chunk 69 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 0.0070 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 overall best weight: 2.1404 ------------------------------------------------------------------------------- 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 = 0.2723 r_free = 0.2723 target = 0.051095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.049650 restraints weight = 38063.630| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 0.66 r_work: 0.2645 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9914 Z= 0.157 Angle : 0.619 12.453 14550 Z= 0.347 Chirality : 0.042 0.478 1759 Planarity : 0.004 0.042 953 Dihedral : 26.963 177.711 4146 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.99 % Favored : 87.80 % Rotamer: Outliers : 7.01 % Allowed : 31.31 % Favored : 61.68 % 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: -2.87 (0.36), residues: 492 helix: -1.58 (0.42), residues: 128 sheet: -1.65 (1.12), residues: 23 loop : -2.20 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 270 TYR 0.011 0.001 TYR D 305 PHE 0.014 0.002 PHE D 453 TRP 0.008 0.001 TRP D 161 HIS 0.002 0.001 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.16 ( 9909) covalent geometry : angle 0.61774 / 0.35 (14545) SS BOND : bond 0.00364 / 0.18 ( 1) SS BOND : angle 0.61940 / 0.89 ( 2) hydrogen bonds : bond 0.07859 / 8.82 ( 254) hydrogen bonds : angle 5.28026 / 5.47 ( 561) metal coordination : bond 0.01391 / 0.82 ( 4) metal coordination : angle 2.99167 / 4.04 ( 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 48 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 18 time to evaluate : 0.219 Fit side-chains REVERT: D 223 GLU cc_start: 0.9326 (OUTLIER) cc_final: 0.8735 (mt-10) REVERT: D 267 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.7374 (pm20) REVERT: D 286 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8015 (tptt) REVERT: D 449 GLU cc_start: 0.9334 (OUTLIER) cc_final: 0.7731 (pp20) REVERT: D 473 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.7064 (tt0) outliers start: 30 outliers final: 24 residues processed: 46 average time/residue: 0.0972 time to fit residues: 6.3571 Evaluate side-chains 47 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 18 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 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 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 449 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 0.4980 chunk 19 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 = 0.2725 r_free = 0.2725 target = 0.051149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.049698 restraints weight = 37951.620| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 0.66 r_work: 0.2646 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1944 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= 0.160 Angle : 0.617 12.557 14550 Z= 0.346 Chirality : 0.042 0.477 1759 Planarity : 0.004 0.042 953 Dihedral : 26.963 177.738 4146 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.99 % Favored : 87.80 % Rotamer: Outliers : 6.78 % Allowed : 32.01 % Favored : 61.21 % 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: -2.86 (0.37), residues: 492 helix: -1.59 (0.42), residues: 128 sheet: -1.66 (1.13), residues: 23 loop : -2.17 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 270 TYR 0.011 0.001 TYR D 340 PHE 0.014 0.002 PHE D 453 TRP 0.009 0.001 TRP D 161 HIS 0.002 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.16 ( 9909) covalent geometry : angle 0.61590 / 0.35 (14545) SS BOND : bond 0.00346 / 0.17 ( 1) SS BOND : angle 0.63214 / 0.93 ( 2) hydrogen bonds : bond 0.07819 / 8.77 ( 254) hydrogen bonds : angle 5.26851 / 5.46 ( 561) metal coordination : bond 0.01451 / 0.85 ( 4) metal coordination : angle 2.98016 / 3.81 ( 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 47 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 18 time to evaluate : 0.222 Fit side-chains REVERT: D 223 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.8741 (mt-10) REVERT: D 267 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.7382 (pm20) REVERT: D 286 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.7987 (tptt) REVERT: D 449 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.7780 (pp20) REVERT: D 473 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.7066 (tt0) outliers start: 29 outliers final: 24 residues processed: 45 average time/residue: 0.0967 time to fit residues: 6.1761 Evaluate side-chains 47 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 18 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 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 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 449 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 46 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.2683 r_free = 0.2683 target = 0.049739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.048300 restraints weight = 39552.090| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 0.68 r_work: 0.2604 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9914 Z= 0.195 Angle : 0.653 12.499 14550 Z= 0.361 Chirality : 0.044 0.490 1759 Planarity : 0.005 0.043 953 Dihedral : 26.956 175.296 4146 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.41 % Favored : 86.38 % Rotamer: Outliers : 6.54 % Allowed : 32.71 % Favored : 60.75 % 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: -1.68 (0.41), residues: 128 sheet: -1.75 (1.14), residues: 23 loop : -2.22 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 270 TYR 0.012 0.002 TYR D 340 PHE 0.013 0.002 PHE D 453 TRP 0.008 0.001 TRP D 161 HIS 0.003 0.001 HIS D 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.19 ( 9909) covalent geometry : angle 0.65095 / 0.36 (14545) SS BOND : bond 0.00306 / 0.15 ( 1) SS BOND : angle 0.63638 / 0.72 ( 2) hydrogen bonds : bond 0.08225 / 9.20 ( 254) hydrogen bonds : angle 5.36143 / 5.56 ( 561) metal coordination : bond 0.02285 / 1.39 ( 4) metal coordination : angle 3.60078 / 4.18 ( 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 : 0.210 Fit side-chains REVERT: D 223 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.8776 (mt-10) REVERT: D 267 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.7414 (pm20) REVERT: D 286 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8015 (tptt) REVERT: D 473 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.7101 (tt0) outliers start: 28 outliers final: 24 residues processed: 44 average time/residue: 0.1002 time to fit residues: 6.2004 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 : 0.258 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 overall best weight: 4.9188 ------------------------------------------------------------------------------- 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 = 0.2628 r_free = 0.2628 target = 0.047778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.046369 restraints weight = 39702.231| |-----------------------------------------------------------------------------| r_work (start): 0.2587 rms_B_bonded: 0.66 r_work: 0.2549 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9914 Z= 0.263 Angle : 0.723 12.555 14550 Z= 0.392 Chirality : 0.048 0.502 1759 Planarity : 0.005 0.043 953 Dihedral : 26.970 173.305 4146 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.82 % Favored : 85.98 % Rotamer: Outliers : 6.54 % Allowed : 32.71 % Favored : 60.75 % 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: -3.16 (0.36), residues: 492 helix: -1.90 (0.39), residues: 134 sheet: -1.83 (1.16), residues: 23 loop : -2.34 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 113 TYR 0.015 0.002 TYR D 344 PHE 0.015 0.002 PHE D 79 TRP 0.007 0.001 TRP D 161 HIS 0.004 0.001 HIS D 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.26 ( 9909) covalent geometry : angle 0.71986 / 0.39 (14545) SS BOND : bond 0.00096 / 0.05 ( 1) SS BOND : angle 0.93800 / 0.88 ( 2) hydrogen bonds : bond 0.08968 / 9.92 ( 254) hydrogen bonds : angle 5.56232 / 5.78 ( 561) metal coordination : bond 0.03259 / 2.00 ( 4) metal coordination : angle 4.49714 / 4.19 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1736.20 seconds wall clock time: 30 minutes 42.96 seconds (1842.96 seconds total)