Starting phenix.real_space_refine on Tue Aug 4 16:14:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lw3_63427/08_2026/9lw3_63427_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lw3_63427/08_2026/9lw3_63427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lw3_63427/08_2026/9lw3_63427_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lw3_63427/08_2026/9lw3_63427_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lw3_63427/08_2026/9lw3_63427.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lw3_63427/08_2026/9lw3_63427.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4 5.49 5 S 32 5.16 5 C 3206 2.51 5 N 658 2.21 5 O 748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4650 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2052 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 1 Chain: "B" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2052 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 1 Chain: "A" Number of atoms: 291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 291 Unusual residues: {' ZN': 1, '4I1': 9, 'CLR': 1, 'LPC': 1, 'PEE': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 251 Unusual residues: {' ZN': 1, '4I1': 7, 'CLR': 1, 'LPC': 1, 'PEE': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 0.97, per 1000 atoms: 0.21 Number of scatterers: 4650 At special positions: 0 Unit cell: (72.39, 89.49, 67.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 32 16.00 P 4 15.00 O 748 8.00 N 658 7.00 C 3206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 240 " distance=2.02 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 240 " distance=2.02 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: 0.26 Conformation dependent library (CDL) restraints added in 91.8 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 34 through 63 removed outlier: 4.504A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 113 Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 121 through 136 removed outlier: 3.528A pdb=" N LEU A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 150 Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.879A pdb=" N LEU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 183 removed outlier: 3.729A pdb=" N ILE A 176 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 195 Processing helix chain 'A' and resid 206 through 222 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 251 through 278 removed outlier: 3.664A pdb=" N LEU A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS A 269 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 15 Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 34 through 63 removed outlier: 4.828A pdb=" N LEU B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 113 Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 121 through 136 removed outlier: 3.516A pdb=" N LEU B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'B' and resid 153 through 161 removed outlier: 3.882A pdb=" N LEU B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 Processing helix chain 'B' and resid 185 through 195 Processing helix chain 'B' and resid 206 through 222 Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 251 through 278 removed outlier: 3.742A pdb=" N LEU B 262 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS B 269 " --> pdb=" O MET B 265 " (cutoff:3.500A) 268 hydrogen bonds defined for protein. 780 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.39 Time building geometry restraints manager: 0.34 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: 1006 1.33 - 1.45: 907 1.45 - 1.56: 2777 1.56 - 1.68: 8 1.68 - 1.80: 52 Bond restraints: 4750 Sorted by residual: bond pdb=" C1 4I1 A 311 " pdb=" O2 4I1 A 311 " ideal model delta sigma weight residual 1.248 1.454 -0.206 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C1 4I1 B 311 " pdb=" O2 4I1 B 311 " ideal model delta sigma weight residual 1.248 1.454 -0.206 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C1 4I1 B 309 " pdb=" O2 4I1 B 309 " ideal model delta sigma weight residual 1.248 1.454 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C1 4I1 A 309 " pdb=" O2 4I1 A 309 " ideal model delta sigma weight residual 1.248 1.454 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C1 4I1 A 313 " pdb=" O2 4I1 A 313 " ideal model delta sigma weight residual 1.248 1.454 -0.206 2.00e-02 2.50e+03 1.06e+02 ... (remaining 4745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.41: 6285 9.41 - 18.81: 45 18.81 - 28.22: 4 28.22 - 37.62: 4 37.62 - 47.03: 4 Bond angle restraints: 6342 Sorted by residual: angle pdb=" O1 4I1 B 308 " pdb=" C1 4I1 B 308 " pdb=" O2 4I1 B 308 " ideal model delta sigma weight residual 126.32 79.29 47.03 3.00e+00 1.11e-01 2.46e+02 angle pdb=" O1 4I1 A 308 " pdb=" C1 4I1 A 308 " pdb=" O2 4I1 A 308 " ideal model delta sigma weight residual 126.32 79.29 47.03 3.00e+00 1.11e-01 2.46e+02 angle pdb=" C2 4I1 B 308 " pdb=" C1 4I1 B 308 " pdb=" O1 4I1 B 308 " ideal model delta sigma weight residual 117.83 159.75 -41.92 3.00e+00 1.11e-01 1.95e+02 angle pdb=" C2 4I1 A 308 " pdb=" C1 4I1 A 308 " pdb=" O1 4I1 A 308 " ideal model delta sigma weight residual 117.83 159.75 -41.92 3.00e+00 1.11e-01 1.95e+02 angle pdb=" C2 4I1 A 308 " pdb=" C1 4I1 A 308 " pdb=" O2 4I1 A 308 " ideal model delta sigma weight residual 115.85 80.46 35.39 3.00e+00 1.11e-01 1.39e+02 ... (remaining 6337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 2517 35.17 - 70.34: 389 70.34 - 105.52: 38 105.52 - 140.69: 10 140.69 - 175.86: 24 Dihedral angle restraints: 2978 sinusoidal: 1480 harmonic: 1498 Sorted by residual: dihedral pdb=" CB CYS B 29 " pdb=" SG CYS B 29 " pdb=" SG CYS B 240 " pdb=" CB CYS B 240 " ideal model delta sinusoidal sigma weight residual -86.00 -153.71 67.71 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" CB CYS A 29 " pdb=" SG CYS A 29 " pdb=" SG CYS A 240 " pdb=" CB CYS A 240 " ideal model delta sinusoidal sigma weight residual -86.00 -151.48 65.48 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" C19 CLR B 303 " pdb=" C10 CLR B 303 " pdb=" C5 CLR B 303 " pdb=" C4 CLR B 303 " ideal model delta sinusoidal sigma weight residual 71.87 -103.99 175.86 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 2975 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.972: 682 0.972 - 1.944: 0 1.944 - 2.916: 2 2.916 - 3.887: 0 3.887 - 4.859: 2 Chirality restraints: 686 Sorted by residual: chirality pdb=" C2 PEE A 303 " pdb=" C1 PEE A 303 " pdb=" C3 PEE A 303 " pdb=" O2 PEE A 303 " both_signs ideal model delta sigma weight residual False -2.33 2.53 -4.86 2.00e-01 2.50e+01 5.90e+02 chirality pdb=" C2 PEE B 304 " pdb=" C1 PEE B 304 " pdb=" C3 PEE B 304 " pdb=" O2 PEE B 304 " both_signs ideal model delta sigma weight residual False -2.33 2.53 -4.86 2.00e-01 2.50e+01 5.90e+02 chirality pdb=" C10 CLR A 302 " pdb=" C1 CLR A 302 " pdb=" C5 CLR A 302 " pdb=" C9 CLR A 302 " both_signs ideal model delta sigma weight residual False -2.85 -0.88 -1.97 2.00e-01 2.50e+01 9.67e+01 ... (remaining 683 not shown) Planarity restraints: 736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5 4I1 A 304 " -0.301 2.00e-02 2.50e+03 3.00e-01 9.01e+02 pdb=" C6 4I1 A 304 " 0.301 2.00e-02 2.50e+03 pdb=" C7 4I1 A 304 " 0.299 2.00e-02 2.50e+03 pdb=" C8 4I1 A 304 " -0.300 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 4I1 B 305 " 0.301 2.00e-02 2.50e+03 3.00e-01 9.01e+02 pdb=" C6 4I1 B 305 " -0.301 2.00e-02 2.50e+03 pdb=" C7 4I1 B 305 " -0.299 2.00e-02 2.50e+03 pdb=" C8 4I1 B 305 " 0.300 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5 4I1 B 306 " 0.271 2.00e-02 2.50e+03 2.71e-01 7.33e+02 pdb=" C6 4I1 B 306 " -0.273 2.00e-02 2.50e+03 pdb=" C7 4I1 B 306 " -0.269 2.00e-02 2.50e+03 pdb=" C8 4I1 B 306 " 0.271 2.00e-02 2.50e+03 ... (remaining 733 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1481 2.83 - 3.35: 4013 3.35 - 3.87: 8205 3.87 - 4.38: 10634 4.38 - 4.90: 15949 Nonbonded interactions: 40282 Sorted by model distance: nonbonded pdb=" N LEU A 184 " pdb=" N TYR A 185 " model vdw 2.315 2.560 nonbonded pdb=" N LEU B 184 " pdb=" N TYR B 185 " model vdw 2.316 2.560 nonbonded pdb=" CE2 PHE B 109 " pdb=" O PHE B 172 " model vdw 2.364 3.340 nonbonded pdb=" N PEE B 304 " pdb=" O4P PEE B 304 " model vdw 2.385 2.496 nonbonded pdb=" N PEE A 303 " pdb=" O4P PEE A 303 " model vdw 2.385 2.496 ... (remaining 40277 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 280 or resid 305 through 311)) selection = (chain 'B' and (resid 2 through 280 or resid 305 through 311)) } 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: 8.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.640 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 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 : 0.020 0.206 4752 Z= 1.107 Angle : 2.568 47.031 6346 Z= 1.140 Chirality : 0.298 4.859 686 Planarity : 0.028 0.300 736 Dihedral : 33.668 175.860 2012 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.59 % Allowed : 9.45 % Favored : 89.96 % Rotamer: Outliers : 23.88 % Allowed : 14.06 % Favored : 62.05 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.32), residues: 508 helix: -1.51 (0.24), residues: 350 sheet: None (None), residues: 0 loop : -3.74 (0.39), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 140 TYR 0.019 0.002 TYR A 177 PHE 0.014 0.002 PHE A 217 TRP 0.008 0.001 TRP A 35 HIS 0.012 0.002 HIS B 259 Details of bonding type rmsd/Z covalent geometry : bond 0.01967 / 1.11 ( 4750) covalent geometry : angle 2.56753 / 1.14 ( 6342) SS BOND : bond 0.00829 / 0.41 ( 2) SS BOND : angle 2.56133 / 1.29 ( 4) hydrogen bonds : bond 0.17540 / 11.19 ( 268) hydrogen bonds : angle 7.50232 / 5.65 ( 780) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 105 time to evaluate : 0.155 Fit side-chains REVERT: A 36 GLN cc_start: 0.6827 (mp10) cc_final: 0.6612 (mp10) REVERT: A 144 VAL cc_start: 0.7718 (t) cc_final: 0.7493 (p) REVERT: A 265 MET cc_start: 0.8112 (mpp) cc_final: 0.7173 (mmt) REVERT: B 36 GLN cc_start: 0.6847 (mp10) cc_final: 0.6623 (mp10) REVERT: B 89 SER cc_start: 0.6886 (OUTLIER) cc_final: 0.6643 (t) REVERT: B 92 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6875 (ttpp) REVERT: B 144 VAL cc_start: 0.7676 (t) cc_final: 0.7427 (p) REVERT: B 265 MET cc_start: 0.8084 (mpp) cc_final: 0.7218 (mmt) outliers start: 107 outliers final: 13 residues processed: 185 average time/residue: 0.3318 time to fit residues: 64.3566 Evaluate side-chains 94 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 CYS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 29 CYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 254 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 236 ASN B 36 GLN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 HIS B 236 ASN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.173016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.146176 restraints weight = 5107.122| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.94 r_work: 0.3674 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4752 Z= 0.181 Angle : 1.718 41.602 6346 Z= 0.627 Chirality : 0.109 1.852 686 Planarity : 0.006 0.033 736 Dihedral : 34.515 167.331 1107 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 8.71 % Allowed : 23.66 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.36), residues: 508 helix: 0.32 (0.26), residues: 356 sheet: None (None), residues: 0 loop : -2.36 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 58 TYR 0.011 0.001 TYR B 177 PHE 0.020 0.002 PHE A 274 TRP 0.013 0.001 TRP B 208 HIS 0.006 0.002 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 ( 4750) covalent geometry : angle 1.71773 / 0.63 ( 6342) SS BOND : bond 0.00365 / 0.18 ( 2) SS BOND : angle 1.75688 / 0.89 ( 4) hydrogen bonds : bond 0.04674 / 3.01 ( 268) hydrogen bonds : angle 5.07836 / 3.87 ( 780) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 0.168 Fit side-chains REVERT: A 40 LEU cc_start: 0.5889 (OUTLIER) cc_final: 0.5488 (tt) REVERT: A 276 TYR cc_start: 0.7418 (m-10) cc_final: 0.7203 (m-10) REVERT: B 40 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5390 (tt) outliers start: 39 outliers final: 11 residues processed: 118 average time/residue: 0.3072 time to fit residues: 38.2651 Evaluate side-chains 86 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 261 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 236 ASN B 7 GLN B 24 ASN B 181 HIS ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.170499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.142365 restraints weight = 5168.459| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.10 r_work: 0.3639 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4752 Z= 0.157 Angle : 1.693 41.787 6346 Z= 0.607 Chirality : 0.107 1.836 686 Planarity : 0.005 0.041 736 Dihedral : 32.343 177.634 1088 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 8.04 % Allowed : 25.67 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.38), residues: 508 helix: 0.95 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -2.00 (0.52), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 168 TYR 0.010 0.001 TYR A 177 PHE 0.012 0.001 PHE B 162 TRP 0.009 0.001 TRP A 208 HIS 0.006 0.002 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 4750) covalent geometry : angle 1.69314 / 0.61 ( 6342) SS BOND : bond 0.00224 / 0.11 ( 2) SS BOND : angle 1.84650 / 0.93 ( 4) hydrogen bonds : bond 0.04207 / 2.71 ( 268) hydrogen bonds : angle 4.62646 / 3.50 ( 780) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 77 time to evaluate : 0.158 Fit side-chains REVERT: A 36 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6828 (mp10) REVERT: A 40 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5525 (tt) REVERT: A 238 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8247 (mmm) REVERT: B 28 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7147 (m-30) REVERT: B 40 LEU cc_start: 0.5731 (OUTLIER) cc_final: 0.5389 (tt) outliers start: 36 outliers final: 15 residues processed: 107 average time/residue: 0.3664 time to fit residues: 41.2235 Evaluate side-chains 90 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 261 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN B 236 ASN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.171118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.142896 restraints weight = 5168.036| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.11 r_work: 0.3586 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4752 Z= 0.162 Angle : 1.677 41.556 6346 Z= 0.601 Chirality : 0.110 1.891 686 Planarity : 0.005 0.039 736 Dihedral : 30.697 172.078 1087 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 8.71 % Allowed : 24.78 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.38), residues: 508 helix: 1.17 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.68 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 58 TYR 0.012 0.001 TYR A 177 PHE 0.010 0.001 PHE B 103 TRP 0.016 0.001 TRP A 35 HIS 0.006 0.002 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 4750) covalent geometry : angle 1.67684 / 0.60 ( 6342) SS BOND : bond 0.00317 / 0.16 ( 2) SS BOND : angle 1.78611 / 0.89 ( 4) hydrogen bonds : bond 0.04079 / 2.63 ( 268) hydrogen bonds : angle 4.45795 / 3.35 ( 780) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 77 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.6941 (mp10) REVERT: A 40 LEU cc_start: 0.5778 (OUTLIER) cc_final: 0.5297 (tt) REVERT: A 62 ARG cc_start: 0.6335 (OUTLIER) cc_final: 0.5302 (ptp-170) REVERT: A 227 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7913 (mp) REVERT: B 28 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7291 (m-30) REVERT: B 40 LEU cc_start: 0.5628 (OUTLIER) cc_final: 0.5206 (tt) REVERT: B 226 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7669 (mt) outliers start: 39 outliers final: 15 residues processed: 113 average time/residue: 0.4177 time to fit residues: 49.4566 Evaluate side-chains 98 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 261 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 236 ASN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN B 236 ASN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.174534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143765 restraints weight = 5050.187| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.29 r_work: 0.3586 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4752 Z= 0.151 Angle : 1.668 41.520 6346 Z= 0.593 Chirality : 0.109 1.868 686 Planarity : 0.005 0.038 736 Dihedral : 29.713 170.110 1087 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 7.81 % Allowed : 25.89 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.39), residues: 508 helix: 1.34 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.52 (0.55), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 58 TYR 0.010 0.001 TYR B 177 PHE 0.015 0.001 PHE B 162 TRP 0.009 0.001 TRP B 255 HIS 0.005 0.002 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 4750) covalent geometry : angle 1.66788 / 0.59 ( 6342) SS BOND : bond 0.00352 / 0.18 ( 2) SS BOND : angle 1.74003 / 0.87 ( 4) hydrogen bonds : bond 0.03873 / 2.49 ( 268) hydrogen bonds : angle 4.34050 / 3.25 ( 780) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 0.161 Fit side-chains REVERT: A 36 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6689 (mp10) REVERT: A 40 LEU cc_start: 0.5389 (OUTLIER) cc_final: 0.4972 (tt) REVERT: A 62 ARG cc_start: 0.6047 (OUTLIER) cc_final: 0.5140 (ptp-170) REVERT: A 253 ARG cc_start: 0.7773 (mtp85) cc_final: 0.7531 (mtp85) REVERT: B 28 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7354 (m-30) REVERT: B 40 LEU cc_start: 0.5247 (OUTLIER) cc_final: 0.4821 (tt) REVERT: B 226 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7302 (mt) outliers start: 35 outliers final: 14 residues processed: 114 average time/residue: 0.4247 time to fit residues: 50.7522 Evaluate side-chains 105 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 261 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN B 236 ASN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.176243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.144711 restraints weight = 5106.291| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.39 r_work: 0.3610 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4752 Z= 0.132 Angle : 1.666 41.491 6346 Z= 0.591 Chirality : 0.109 1.871 686 Planarity : 0.005 0.037 736 Dihedral : 29.037 179.249 1087 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 7.81 % Allowed : 25.89 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.39), residues: 508 helix: 1.49 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.55 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 58 TYR 0.010 0.001 TYR A 14 PHE 0.017 0.001 PHE B 274 TRP 0.011 0.001 TRP A 35 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 4750) covalent geometry : angle 1.66651 / 0.59 ( 6342) SS BOND : bond 0.00268 / 0.13 ( 2) SS BOND : angle 1.58473 / 0.79 ( 4) hydrogen bonds : bond 0.03713 / 2.41 ( 268) hydrogen bonds : angle 4.26337 / 3.20 ( 780) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.109 Fit side-chains revert: symmetry clash REVERT: A 37 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: A 40 LEU cc_start: 0.5426 (OUTLIER) cc_final: 0.5014 (tt) REVERT: A 62 ARG cc_start: 0.5981 (OUTLIER) cc_final: 0.5129 (ptp-170) REVERT: B 40 LEU cc_start: 0.5226 (OUTLIER) cc_final: 0.4813 (tt) REVERT: B 62 ARG cc_start: 0.6015 (OUTLIER) cc_final: 0.5202 (ptp-170) REVERT: B 154 ASN cc_start: 0.7393 (m-40) cc_final: 0.6695 (m-40) REVERT: B 226 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7265 (mt) REVERT: B 263 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7309 (ttp) outliers start: 35 outliers final: 18 residues processed: 112 average time/residue: 0.4378 time to fit residues: 51.2331 Evaluate side-chains 104 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 37 GLN Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 263 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.175136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143922 restraints weight = 4977.945| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.30 r_work: 0.3594 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4752 Z= 0.156 Angle : 1.675 41.486 6346 Z= 0.595 Chirality : 0.109 1.859 686 Planarity : 0.005 0.040 736 Dihedral : 27.700 171.396 1087 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 7.81 % Allowed : 25.89 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.38), residues: 508 helix: 1.51 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.51 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 58 TYR 0.010 0.001 TYR A 14 PHE 0.009 0.001 PHE B 103 TRP 0.006 0.001 TRP A 208 HIS 0.005 0.002 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 4750) covalent geometry : angle 1.67480 / 0.60 ( 6342) SS BOND : bond 0.00353 / 0.18 ( 2) SS BOND : angle 1.81859 / 0.92 ( 4) hydrogen bonds : bond 0.03809 / 2.45 ( 268) hydrogen bonds : angle 4.27424 / 3.21 ( 780) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.5580 (OUTLIER) cc_final: 0.5082 (tt) REVERT: A 62 ARG cc_start: 0.5978 (OUTLIER) cc_final: 0.5147 (ptp-170) REVERT: B 40 LEU cc_start: 0.5319 (OUTLIER) cc_final: 0.4884 (tt) REVERT: B 62 ARG cc_start: 0.6047 (OUTLIER) cc_final: 0.5277 (ptp-170) REVERT: B 154 ASN cc_start: 0.7487 (m-40) cc_final: 0.6789 (m-40) REVERT: B 226 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.7229 (mt) REVERT: B 263 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7272 (ttp) outliers start: 35 outliers final: 18 residues processed: 110 average time/residue: 0.4017 time to fit residues: 46.3428 Evaluate side-chains 102 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 263 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 36 GLN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN B 236 ASN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.175570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.143117 restraints weight = 5116.126| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.48 r_work: 0.3665 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4752 Z= 0.141 Angle : 1.669 41.514 6346 Z= 0.591 Chirality : 0.108 1.858 686 Planarity : 0.005 0.034 736 Dihedral : 26.900 171.525 1087 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 6.03 % Allowed : 27.46 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.38), residues: 508 helix: 1.59 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.47 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 58 TYR 0.010 0.001 TYR A 14 PHE 0.021 0.001 PHE A 274 TRP 0.006 0.001 TRP A 208 HIS 0.006 0.002 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4750) covalent geometry : angle 1.66859 / 0.59 ( 6342) SS BOND : bond 0.00292 / 0.15 ( 2) SS BOND : angle 1.59168 / 0.80 ( 4) hydrogen bonds : bond 0.03725 / 2.41 ( 268) hydrogen bonds : angle 4.22617 / 3.17 ( 780) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.6930 (mp10) REVERT: A 40 LEU cc_start: 0.5767 (OUTLIER) cc_final: 0.5300 (tt) REVERT: A 62 ARG cc_start: 0.6086 (OUTLIER) cc_final: 0.5299 (ptp-170) REVERT: B 40 LEU cc_start: 0.5596 (OUTLIER) cc_final: 0.5155 (tt) REVERT: B 62 ARG cc_start: 0.6075 (OUTLIER) cc_final: 0.5313 (ptp-170) REVERT: B 154 ASN cc_start: 0.7624 (m-40) cc_final: 0.6951 (m-40) REVERT: B 226 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7483 (mt) REVERT: B 227 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7686 (mp) REVERT: B 263 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7307 (ttp) outliers start: 27 outliers final: 17 residues processed: 106 average time/residue: 0.4118 time to fit residues: 45.6194 Evaluate side-chains 106 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 263 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.0670 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 0.0570 chunk 44 optimal weight: 0.5980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.175892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144027 restraints weight = 4983.954| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.44 r_work: 0.3666 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4752 Z= 0.117 Angle : 1.662 41.500 6346 Z= 0.586 Chirality : 0.108 1.865 686 Planarity : 0.005 0.034 736 Dihedral : 26.373 171.477 1087 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 6.03 % Allowed : 27.68 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.39), residues: 508 helix: 1.72 (0.28), residues: 360 sheet: None (None), residues: 0 loop : -1.44 (0.53), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 168 TYR 0.010 0.001 TYR A 14 PHE 0.008 0.001 PHE B 103 TRP 0.007 0.001 TRP A 35 HIS 0.005 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 4750) covalent geometry : angle 1.66208 / 0.59 ( 6342) SS BOND : bond 0.00229 / 0.11 ( 2) SS BOND : angle 1.41285 / 0.71 ( 4) hydrogen bonds : bond 0.03561 / 2.31 ( 268) hydrogen bonds : angle 4.16876 / 3.14 ( 780) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.5845 (OUTLIER) cc_final: 0.5355 (tt) REVERT: A 62 ARG cc_start: 0.6012 (OUTLIER) cc_final: 0.5225 (ptp-170) REVERT: B 40 LEU cc_start: 0.5660 (OUTLIER) cc_final: 0.5203 (tt) REVERT: B 62 ARG cc_start: 0.6010 (OUTLIER) cc_final: 0.5282 (ptp-170) REVERT: B 154 ASN cc_start: 0.7592 (m-40) cc_final: 0.6898 (m-40) REVERT: B 226 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7388 (mp) REVERT: B 263 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7262 (ttp) outliers start: 27 outliers final: 16 residues processed: 103 average time/residue: 0.4051 time to fit residues: 43.5713 Evaluate side-chains 99 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 263 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 36 GLN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN B 236 ASN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.174372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.142393 restraints weight = 5045.890| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.38 r_work: 0.3666 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4752 Z= 0.155 Angle : 1.676 41.505 6346 Z= 0.595 Chirality : 0.108 1.851 686 Planarity : 0.005 0.038 736 Dihedral : 25.969 172.320 1087 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 6.47 % Allowed : 27.23 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.38), residues: 508 helix: 1.62 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.41 (0.52), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 168 TYR 0.011 0.001 TYR A 248 PHE 0.022 0.001 PHE A 274 TRP 0.009 0.001 TRP A 255 HIS 0.005 0.002 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 4750) covalent geometry : angle 1.67601 / 0.60 ( 6342) SS BOND : bond 0.00277 / 0.14 ( 2) SS BOND : angle 1.58561 / 0.78 ( 4) hydrogen bonds : bond 0.03807 / 2.46 ( 268) hydrogen bonds : angle 4.20980 / 3.16 ( 780) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.100 Fit side-chains REVERT: A 36 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6884 (mp10) REVERT: A 40 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5400 (tt) REVERT: A 62 ARG cc_start: 0.6061 (OUTLIER) cc_final: 0.5293 (ptp-170) REVERT: B 40 LEU cc_start: 0.5748 (OUTLIER) cc_final: 0.5261 (tt) REVERT: B 62 ARG cc_start: 0.5999 (OUTLIER) cc_final: 0.5306 (ptp-170) REVERT: B 154 ASN cc_start: 0.7648 (m-40) cc_final: 0.6954 (m-40) REVERT: B 198 TYR cc_start: 0.8284 (m-80) cc_final: 0.7916 (m-80) REVERT: B 226 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7523 (mt) REVERT: B 263 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7298 (ttp) outliers start: 29 outliers final: 18 residues processed: 109 average time/residue: 0.4598 time to fit residues: 52.2953 Evaluate side-chains 105 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 263 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN B 236 ASN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.176312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.143901 restraints weight = 5028.318| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.41 r_work: 0.3633 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 4752 Z= 0.301 Angle : 2.208 59.194 6346 Z= 1.082 Chirality : 0.109 1.852 686 Planarity : 0.005 0.049 736 Dihedral : 25.988 172.308 1087 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.13 % Favored : 95.67 % Rotamer: Outliers : 5.58 % Allowed : 28.12 % Favored : 66.29 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.38), residues: 508 helix: 1.60 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.54 (0.52), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 58 TYR 0.010 0.001 TYR A 248 PHE 0.012 0.001 PHE A 274 TRP 0.008 0.001 TRP A 255 HIS 0.005 0.002 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.30 ( 4750) covalent geometry : angle 2.20786 / 1.08 ( 6342) SS BOND : bond 0.00280 / 0.14 ( 2) SS BOND : angle 1.56898 / 0.78 ( 4) hydrogen bonds : bond 0.03796 / 2.46 ( 268) hydrogen bonds : angle 4.21168 / 3.16 ( 780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1751.58 seconds wall clock time: 30 minutes 38.61 seconds (1838.61 seconds total)