Starting phenix.real_space_refine on Wed Feb 4 06:13:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lir_63121/02_2026/9lir_63121.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lir_63121/02_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_63121/02_2026/9lir_63121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lir_63121/02_2026/9lir_63121.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lir_63121/02_2026/9lir_63121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lir_63121/02_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-2.0-5952/lib/python3.9/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: 1.78, per 1000 atoms: 0.19 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: 0.79 Conformation dependent library (CDL) restraints added in 175.4 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: 1.07 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: 1.63 Time building geometry restraints manager: 1.02 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=" C ILE D 303 " pdb=" N PRO D 304 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.20e-02 6.94e+03 4.97e+00 bond pdb=" C3' U A 29 " pdb=" O3' U A 29 " ideal model delta sigma weight residual 1.427 1.454 -0.027 1.50e-02 4.44e+03 3.12e+00 bond pdb=" C3' DG B 9 " pdb=" O3' DG B 9 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.10e+00 bond pdb=" C3' DT C 26 " pdb=" O3' DT C 26 " ideal model delta sigma weight residual 1.422 1.468 -0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" C LEU D 296 " pdb=" N SER D 297 " ideal model delta sigma weight residual 1.332 1.312 0.021 1.40e-02 5.10e+03 2.18e+00 ... (remaining 9904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 14372 3.00 - 6.01: 150 6.01 - 9.01: 21 9.01 - 12.02: 1 12.02 - 15.02: 1 Bond angle restraints: 14545 Sorted by residual: angle pdb=" C3' U A 29 " pdb=" O3' U A 29 " pdb=" P G A 30 " ideal model delta sigma weight residual 120.20 126.91 -6.71 1.50e+00 4.44e-01 2.00e+01 angle pdb=" CA LEU D 170 " pdb=" CB LEU D 170 " pdb=" CG LEU D 170 " ideal model delta sigma weight residual 116.30 131.32 -15.02 3.50e+00 8.16e-02 1.84e+01 angle pdb=" CA VAL D 70 " pdb=" CB VAL D 70 " pdb=" CG1 VAL D 70 " ideal model delta sigma weight residual 110.40 117.38 -6.98 1.70e+00 3.46e-01 1.69e+01 angle pdb=" C ALA D 343 " pdb=" N TYR D 344 " pdb=" CA TYR D 344 " ideal model delta sigma weight residual 120.38 125.86 -5.48 1.37e+00 5.33e-01 1.60e+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 3.00e+00 1.11e-01 1.28e+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: 1481 0.049 - 0.099: 208 0.099 - 0.148: 52 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 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 : 0.003 0.053 9914 Z= 0.179 Angle : 0.825 15.019 14550 Z= 0.426 Chirality : 0.041 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 covalent geometry : bond 0.00338 ( 9909) covalent geometry : angle 0.82244 (14545) SS BOND : bond 0.01042 ( 1) SS BOND : angle 0.38112 ( 2) hydrogen bonds : bond 0.12961 ( 254) hydrogen bonds : angle 7.30114 ( 561) metal coordination : bond 0.01187 ( 4) metal coordination : angle 4.71278 ( 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 : 0.216 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: 0.1087 time to fit residues: 5.9917 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 : 0.142 ------------------------------------------------------------------------------- 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: 10.0000 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.056562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.054989 restraints weight = 38746.069| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 0.73 r_work: 0.2783 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.0765 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= 0.139 Angle : 0.646 12.181 14550 Z= 0.332 Chirality : 0.035 0.203 1759 Planarity : 0.004 0.045 953 Dihedral : 26.850 178.986 4168 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.98 % Favored : 88.82 % Rotamer: Outliers : 5.61 % Allowed : 29.44 % Favored : 64.95 % 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: -3.04 (0.36), residues: 492 helix: -1.84 (0.40), residues: 135 sheet: -1.72 (1.11), residues: 23 loop : -2.25 (0.33), residues: 334 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 0.019 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 covalent geometry : bond 0.00275 ( 9909) covalent geometry : angle 0.64414 (14545) SS BOND : bond 0.00446 ( 1) SS BOND : angle 0.79124 ( 2) hydrogen bonds : bond 0.06390 ( 254) hydrogen bonds : angle 5.17041 ( 561) metal coordination : bond 0.01013 ( 4) metal coordination : angle 3.15268 ( 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 44 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 20 time to evaluate : 0.176 Fit side-chains REVERT: D 216 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9097 (pp) REVERT: D 473 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.6551 (tt0) outliers start: 24 outliers final: 11 residues processed: 42 average time/residue: 0.0759 time to fit residues: 4.7689 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 : 0.185 ------------------------------------------------------------------------------- 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 345 CYS 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 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: 8.9990 chunk 52 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 53 optimal weight: 0.4980 chunk 37 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 0.0870 chunk 64 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2759 r_free = 0.2759 target = 0.052454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.050993 restraints weight = 38697.978| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 0.68 r_work: 0.2682 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9914 Z= 0.171 Angle : 0.670 12.124 14550 Z= 0.340 Chirality : 0.036 0.188 1759 Planarity : 0.004 0.040 953 Dihedral : 26.896 174.994 4154 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.20 % Favored : 87.60 % Rotamer: Outliers : 4.21 % Allowed : 31.54 % Favored : 64.25 % 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: -2.83 (0.36), residues: 492 helix: -1.54 (0.42), residues: 128 sheet: -1.48 (1.14), residues: 23 loop : -2.18 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 113 TYR 0.009 0.001 TYR D 340 PHE 0.016 0.002 PHE D 453 TRP 0.011 0.001 TRP D 161 HIS 0.002 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9909) covalent geometry : angle 0.66761 (14545) SS BOND : bond 0.00442 ( 1) SS BOND : angle 0.50224 ( 2) hydrogen bonds : bond 0.06139 ( 254) hydrogen bonds : angle 5.07824 ( 561) metal coordination : bond 0.01613 ( 4) metal coordination : angle 3.96006 ( 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 38 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 20 time to evaluate : 0.211 Fit side-chains REVERT: D 473 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.6961 (tt0) outliers start: 18 outliers final: 12 residues processed: 36 average time/residue: 0.0755 time to fit residues: 3.9861 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 : 0.209 ------------------------------------------------------------------------------- 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 142 CYS Chi-restraints excluded: chain D residue 216 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 453 PHE Chi-restraints excluded: chain D residue 473 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2757 r_free = 0.2757 target = 0.052645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.051102 restraints weight = 39967.716| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 0.71 r_work: 0.2678 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9914 Z= 0.150 Angle : 0.647 12.309 14550 Z= 0.329 Chirality : 0.035 0.192 1759 Planarity : 0.004 0.039 953 Dihedral : 26.891 175.856 4146 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.99 % Favored : 87.80 % Rotamer: Outliers : 6.07 % Allowed : 32.24 % 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: -2.90 (0.36), residues: 492 helix: -1.62 (0.41), residues: 134 sheet: -1.54 (1.12), residues: 23 loop : -2.22 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 84 TYR 0.009 0.001 TYR D 340 PHE 0.016 0.001 PHE D 453 TRP 0.012 0.001 TRP D 161 HIS 0.002 0.001 HIS D 104 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9909) covalent geometry : angle 0.64551 (14545) SS BOND : bond 0.00428 ( 1) SS BOND : angle 0.60381 ( 2) hydrogen bonds : bond 0.06011 ( 254) hydrogen bonds : angle 5.02990 ( 561) metal coordination : bond 0.01069 ( 4) metal coordination : angle 3.15820 ( 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: 26 poor density : 20 time to evaluate : 0.151 Fit side-chains REVERT: D 216 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9135 (pp) REVERT: D 286 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.7890 (tptt) REVERT: D 449 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.7222 (pp20) REVERT: D 473 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.6888 (tt0) outliers start: 26 outliers final: 18 residues processed: 42 average time/residue: 0.0864 time to fit residues: 5.1540 Evaluate side-chains 41 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 19 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 193 LEU Chi-restraints excluded: chain D residue 211 TYR Chi-restraints excluded: chain D residue 216 LEU 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 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 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: 10.0000 chunk 68 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2652 r_free = 0.2652 target = 0.048579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.047167 restraints weight = 39121.483| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 0.66 r_work: 0.2574 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9914 Z= 0.258 Angle : 0.733 12.531 14550 Z= 0.369 Chirality : 0.039 0.205 1759 Planarity : 0.005 0.042 953 Dihedral : 27.016 179.660 4146 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.43 % Favored : 85.37 % Rotamer: Outliers : 7.01 % Allowed : 31.78 % 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: -2.94 (0.36), residues: 492 helix: -1.70 (0.40), residues: 134 sheet: -1.57 (1.14), residues: 23 loop : -2.22 (0.34), residues: 335 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 0.015 0.002 PHE D 453 TRP 0.009 0.001 TRP D 161 HIS 0.003 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 9909) covalent geometry : angle 0.73052 (14545) SS BOND : bond 0.00202 ( 1) SS BOND : angle 0.76108 ( 2) hydrogen bonds : bond 0.07066 ( 254) hydrogen bonds : angle 5.34708 ( 561) metal coordination : bond 0.02475 ( 4) metal coordination : angle 4.34314 ( 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 48 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 18 time to evaluate : 0.178 Fit side-chains REVERT: D 223 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.8790 (mt-10) REVERT: D 267 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.7407 (pm20) REVERT: D 286 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8032 (tptt) REVERT: D 473 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.7146 (tt0) outliers start: 30 outliers final: 21 residues processed: 45 average time/residue: 0.0795 time to fit residues: 5.0838 Evaluate side-chains 43 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 18 time to evaluate : 0.156 ------------------------------------------------------------------------------- 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 162 LEU 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 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 366 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 24 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 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: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2658 r_free = 0.2658 target = 0.048836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.047409 restraints weight = 39745.561| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 0.68 r_work: 0.2580 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9914 Z= 0.235 Angle : 0.712 12.803 14550 Z= 0.360 Chirality : 0.039 0.201 1759 Planarity : 0.004 0.043 953 Dihedral : 27.025 179.577 4146 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.80 % Favored : 86.99 % Rotamer: Outliers : 6.31 % Allowed : 32.94 % 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: -2.99 (0.36), residues: 492 helix: -1.71 (0.41), residues: 128 sheet: -1.64 (1.16), residues: 23 loop : -2.27 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 113 TYR 0.011 0.001 TYR D 340 PHE 0.014 0.002 PHE D 453 TRP 0.012 0.001 TRP D 161 HIS 0.004 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 9909) covalent geometry : angle 0.71053 (14545) SS BOND : bond 0.00243 ( 1) SS BOND : angle 0.63911 ( 2) hydrogen bonds : bond 0.06796 ( 254) hydrogen bonds : angle 5.36439 ( 561) metal coordination : bond 0.02303 ( 4) metal coordination : angle 3.69756 ( 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 45 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 18 time to evaluate : 0.172 Fit side-chains REVERT: D 223 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.8780 (mt-10) REVERT: D 267 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.7408 (pm20) REVERT: D 286 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8022 (tptt) REVERT: D 473 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.7133 (tt0) outliers start: 27 outliers final: 22 residues processed: 42 average time/residue: 0.0935 time to fit residues: 5.5026 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 : 0.222 ------------------------------------------------------------------------------- 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 162 LEU 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 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 366 MET 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 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: 8.9990 chunk 65 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2659 r_free = 0.2659 target = 0.048847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.047422 restraints weight = 39842.114| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 0.67 r_work: 0.2580 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9914 Z= 0.227 Angle : 0.709 12.909 14550 Z= 0.358 Chirality : 0.038 0.204 1759 Planarity : 0.004 0.043 953 Dihedral : 27.032 179.713 4146 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.82 % Favored : 85.98 % Rotamer: Outliers : 7.01 % Allowed : 32.48 % 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: -2.98 (0.36), residues: 492 helix: -1.70 (0.41), residues: 128 sheet: -1.67 (1.16), residues: 23 loop : -2.26 (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 0.014 0.002 PHE D 453 TRP 0.012 0.001 TRP D 161 HIS 0.004 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 9909) covalent geometry : angle 0.70689 (14545) SS BOND : bond 0.00270 ( 1) SS BOND : angle 0.64832 ( 2) hydrogen bonds : bond 0.06754 ( 254) hydrogen bonds : angle 5.37614 ( 561) metal coordination : bond 0.02070 ( 4) metal coordination : angle 3.50619 ( 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 48 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 18 time to evaluate : 0.144 Fit side-chains REVERT: D 223 GLU cc_start: 0.9355 (OUTLIER) cc_final: 0.8780 (mt-10) REVERT: D 267 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.7409 (pm20) REVERT: D 286 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8041 (tptt) REVERT: D 473 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.7132 (tt0) outliers start: 30 outliers final: 23 residues processed: 45 average time/residue: 0.0984 time to fit residues: 6.1749 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 : 0.133 ------------------------------------------------------------------------------- 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 162 LEU 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 366 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 0.2980 chunk 69 optimal weight: 0.3980 chunk 59 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 28 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 260 ASN ** 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 = 0.052817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.051268 restraints weight = 39818.403| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 0.72 r_work: 0.2682 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9914 Z= 0.134 Angle : 0.649 12.916 14550 Z= 0.332 Chirality : 0.035 0.215 1759 Planarity : 0.004 0.041 953 Dihedral : 26.953 175.518 4146 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.18 % Favored : 88.62 % Rotamer: Outliers : 6.31 % Allowed : 32.94 % 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: -2.97 (0.36), residues: 492 helix: -1.68 (0.41), residues: 134 sheet: -1.60 (1.13), residues: 23 loop : -2.26 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 155 TYR 0.010 0.001 TYR D 305 PHE 0.016 0.001 PHE D 453 TRP 0.016 0.001 TRP D 161 HIS 0.002 0.001 HIS D 243 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9909) covalent geometry : angle 0.64799 (14545) SS BOND : bond 0.00419 ( 1) SS BOND : angle 0.78986 ( 2) hydrogen bonds : bond 0.05987 ( 254) hydrogen bonds : angle 5.10316 ( 561) metal coordination : bond 0.00492 ( 4) metal coordination : angle 2.80486 ( 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 47 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 20 time to evaluate : 0.171 Fit side-chains REVERT: D 216 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9131 (pp) REVERT: D 267 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.7392 (pm20) REVERT: D 286 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.7926 (tptt) REVERT: D 473 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7042 (tt0) outliers start: 27 outliers final: 19 residues processed: 43 average time/residue: 0.0849 time to fit residues: 5.2324 Evaluate side-chains 42 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 19 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 170 LEU Chi-restraints excluded: chain D residue 211 TYR Chi-restraints excluded: chain D residue 216 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2632 r_free = 0.2632 target = 0.047916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.046505 restraints weight = 39642.315| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 0.67 r_work: 0.2554 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9914 Z= 0.298 Angle : 0.758 12.928 14550 Z= 0.380 Chirality : 0.041 0.218 1759 Planarity : 0.005 0.043 953 Dihedral : 27.017 178.016 4146 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.63 % Favored : 85.16 % Rotamer: Outliers : 5.37 % Allowed : 33.88 % 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: -3.09 (0.37), residues: 492 helix: -1.75 (0.40), residues: 134 sheet: -2.49 (0.92), residues: 33 loop : -2.25 (0.35), residues: 325 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 0.009 0.001 TRP D 161 HIS 0.006 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 9909) covalent geometry : angle 0.75650 (14545) SS BOND : bond 0.00120 ( 1) SS BOND : angle 0.85825 ( 2) hydrogen bonds : bond 0.07257 ( 254) hydrogen bonds : angle 5.42214 ( 561) metal coordination : bond 0.03050 ( 4) metal coordination : angle 3.86475 ( 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 41 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 18 time to evaluate : 0.141 Fit side-chains REVERT: D 68 MET cc_start: 0.9503 (mtt) cc_final: 0.9271 (mtt) REVERT: D 216 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9204 (pp) REVERT: D 267 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: D 286 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.7945 (tptt) REVERT: D 473 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.7124 (tt0) outliers start: 23 outliers final: 18 residues processed: 39 average time/residue: 0.1019 time to fit residues: 5.5719 Evaluate side-chains 40 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 18 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain D residue 211 TYR Chi-restraints excluded: chain D residue 216 LEU 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 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 Chi-restraints excluded: chain D residue 482 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 46 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2626 r_free = 0.2626 target = 0.047663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.046246 restraints weight = 40105.637| |-----------------------------------------------------------------------------| r_work (start): 0.2585 rms_B_bonded: 0.68 r_work: 0.2548 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 2.07 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9914 Z= 0.279 Angle : 0.747 12.889 14550 Z= 0.376 Chirality : 0.041 0.218 1759 Planarity : 0.005 0.043 953 Dihedral : 27.045 175.483 4146 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.02 % Favored : 85.77 % Rotamer: Outliers : 5.14 % Allowed : 34.11 % 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: -3.14 (0.36), residues: 492 helix: -1.86 (0.40), residues: 134 sheet: -1.77 (1.17), residues: 23 loop : -2.35 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 113 TYR 0.011 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 173 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 9909) covalent geometry : angle 0.74496 (14545) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.76016 ( 2) hydrogen bonds : bond 0.07132 ( 254) hydrogen bonds : angle 5.51591 ( 561) metal coordination : bond 0.02754 ( 4) metal coordination : angle 3.98267 ( 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 40 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 18 time to evaluate : 0.166 Fit side-chains REVERT: D 216 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9203 (pp) REVERT: D 267 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.7371 (pm20) REVERT: D 286 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8044 (tptt) REVERT: D 473 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.7174 (tt0) outliers start: 22 outliers final: 17 residues processed: 38 average time/residue: 0.0851 time to fit residues: 4.7304 Evaluate side-chains 39 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 18 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 0.0870 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.048501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.047081 restraints weight = 38976.864| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 0.66 r_work: 0.2572 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9914 Z= 0.207 Angle : 0.712 12.666 14550 Z= 0.361 Chirality : 0.039 0.243 1759 Planarity : 0.004 0.042 953 Dihedral : 27.073 176.760 4146 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.01 % Favored : 86.79 % Rotamer: Outliers : 5.37 % Allowed : 33.88 % 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: -3.07 (0.36), residues: 492 helix: -1.82 (0.40), residues: 134 sheet: -1.77 (1.17), residues: 23 loop : -2.30 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 113 TYR 0.016 0.001 TYR D 305 PHE 0.014 0.002 PHE D 453 TRP 0.007 0.001 TRP D 161 HIS 0.003 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 9909) covalent geometry : angle 0.71090 (14545) SS BOND : bond 0.00366 ( 1) SS BOND : angle 0.52539 ( 2) hydrogen bonds : bond 0.06801 ( 254) hydrogen bonds : angle 5.48152 ( 561) metal coordination : bond 0.01817 ( 4) metal coordination : angle 3.25401 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1495.96 seconds wall clock time: 26 minutes 31.75 seconds (1591.75 seconds total)