Starting phenix.real_space_refine on Thu Jul 2 03:27:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zaq_39884/07_2026/8zaq_39884_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zaq_39884/07_2026/8zaq_39884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zaq_39884/07_2026/8zaq_39884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zaq_39884/07_2026/8zaq_39884.map" model { file = "/net/cci-nas-00/data/ceres_data/8zaq_39884/07_2026/8zaq_39884_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zaq_39884/07_2026/8zaq_39884_neut.cif" } resolution = 2.6 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 24 8.98 5 S 57 5.16 5 C 4327 2.51 5 N 965 2.21 5 O 1076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6449 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2110 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "B" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2110 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 16, 'TRANS': 242} Chain: "C" Number of atoms: 2106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2106 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 16, 'TRANS': 241} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 21 Ad-hoc single atom residues: {' K': 8} Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Chain breaks: 8 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 21 Ad-hoc single atom residues: {' K': 8} Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Chain breaks: 8 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 21 Ad-hoc single atom residues: {' K': 8} Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Chain breaks: 8 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 1.43, per 1000 atoms: 0.22 Number of scatterers: 6449 At special positions: 0 Unit cell: (74.55, 74.2, 79.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 24 19.00 S 57 16.00 O 1076 8.00 N 965 7.00 C 4327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 317.1 milliseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1434 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 74.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 21 through 50 removed outlier: 3.750A pdb=" N GLY A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 68 through 90 Processing helix chain 'A' and resid 105 through 122 Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 178 removed outlier: 3.753A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Proline residue: A 164 - end of helix removed outlier: 3.510A pdb=" N ARG A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 199 Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.515A pdb=" N ILE A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 50 removed outlier: 3.750A pdb=" N GLY B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 105 through 122 Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 178 removed outlier: 3.751A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Proline residue: B 164 - end of helix removed outlier: 3.569A pdb=" N LEU B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 199 Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.506A pdb=" N ILE B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 49 Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 105 through 122 Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 178 removed outlier: 3.750A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Proline residue: C 164 - end of helix removed outlier: 3.518A pdb=" N ARG C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 199 Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.522A pdb=" N ILE C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE C 208 " --> pdb=" O ILE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 427 hydrogen bonds defined for protein. 1272 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: 0.83 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1774 1.34 - 1.46: 1546 1.46 - 1.57: 3242 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 6640 Sorted by residual: bond pdb=" CA PHE A 202 " pdb=" C PHE A 202 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.23e-02 6.61e+03 7.84e-01 bond pdb=" CA PHE B 202 " pdb=" C PHE B 202 " ideal model delta sigma weight residual 1.520 1.531 -0.010 1.23e-02 6.61e+03 7.18e-01 bond pdb=" CA GLY C 158 " pdb=" C GLY C 158 " ideal model delta sigma weight residual 1.516 1.507 0.009 1.12e-02 7.97e+03 6.77e-01 bond pdb=" C LEU A 49 " pdb=" N GLY A 50 " ideal model delta sigma weight residual 1.321 1.331 -0.011 1.30e-02 5.92e+03 6.55e-01 bond pdb=" CA PHE C 202 " pdb=" C PHE C 202 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.50e-01 ... (remaining 6635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 8777 1.48 - 2.96: 232 2.96 - 4.44: 25 4.44 - 5.92: 13 5.92 - 7.39: 2 Bond angle restraints: 9049 Sorted by residual: angle pdb=" C GLY A 93 " pdb=" N THR A 94 " pdb=" CA THR A 94 " ideal model delta sigma weight residual 120.49 127.88 -7.39 1.42e+00 4.96e-01 2.71e+01 angle pdb=" C GLY C 93 " pdb=" N THR C 94 " pdb=" CA THR C 94 " ideal model delta sigma weight residual 120.49 127.67 -7.18 1.42e+00 4.96e-01 2.55e+01 angle pdb=" N VAL C 107 " pdb=" CA VAL C 107 " pdb=" C VAL C 107 " ideal model delta sigma weight residual 113.00 108.95 4.05 1.30e+00 5.92e-01 9.69e+00 angle pdb=" N VAL A 107 " pdb=" CA VAL A 107 " pdb=" C VAL A 107 " ideal model delta sigma weight residual 113.00 109.21 3.79 1.30e+00 5.92e-01 8.49e+00 angle pdb=" N VAL B 107 " pdb=" CA VAL B 107 " pdb=" C VAL B 107 " ideal model delta sigma weight residual 113.00 109.37 3.63 1.30e+00 5.92e-01 7.82e+00 ... (remaining 9044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.46: 3342 22.46 - 44.93: 303 44.93 - 67.39: 52 67.39 - 89.85: 6 89.85 - 112.31: 3 Dihedral angle restraints: 3706 sinusoidal: 1452 harmonic: 2254 Sorted by residual: dihedral pdb=" C1 RET B 309 " pdb=" C2 RET B 309 " pdb=" C3 RET B 309 " pdb=" C4 RET B 309 " ideal model delta sinusoidal sigma weight residual -62.54 49.77 -112.31 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C1 RET C 309 " pdb=" C2 RET C 309 " pdb=" C3 RET C 309 " pdb=" C4 RET C 309 " ideal model delta sinusoidal sigma weight residual -62.54 49.71 -112.25 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C1 RET A 309 " pdb=" C2 RET A 309 " pdb=" C3 RET A 309 " pdb=" C4 RET A 309 " ideal model delta sinusoidal sigma weight residual -62.54 49.63 -112.17 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 3703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 521 0.028 - 0.055: 274 0.055 - 0.083: 96 0.083 - 0.111: 31 0.111 - 0.138: 8 Chirality restraints: 930 Sorted by residual: chirality pdb=" CA THR B 110 " pdb=" N THR B 110 " pdb=" C THR B 110 " pdb=" CB THR B 110 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA THR C 110 " pdb=" N THR C 110 " pdb=" C THR C 110 " pdb=" CB THR C 110 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 927 not shown) Planarity restraints: 1111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 181 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO C 182 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 182 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 182 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 181 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.87e+00 pdb=" N PRO B 182 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 182 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 182 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 181 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO A 182 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 182 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 182 " -0.023 5.00e-02 4.00e+02 ... (remaining 1108 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.90: 6 1.90 - 2.71: 224 2.71 - 3.52: 11554 3.52 - 4.33: 22374 4.33 - 5.14: 37445 Nonbonded interactions: 71603 Sorted by model distance: nonbonded pdb=" K K B 305 " pdb=" O HOH B 409 " model vdw 1.092 3.590 nonbonded pdb=" K K C 305 " pdb=" O HOH C 409 " model vdw 1.094 3.590 nonbonded pdb=" K K A 305 " pdb=" O HOH A 409 " model vdw 1.098 3.590 nonbonded pdb=" CE2 PHE B 195 " pdb=" O HOH B 412 " model vdw 1.863 3.340 nonbonded pdb=" CE2 PHE A 195 " pdb=" O HOH A 412 " model vdw 1.869 3.340 ... (remaining 71598 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 49 or resid 51 through 309)) selection = (chain 'B' and (resid 2 through 49 or resid 51 through 309)) selection = chain 'C' } 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: 18.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.700 Find NCS groups from input model: 0.100 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:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 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 0.030 6643 Z= 0.161 Angle : 0.587 7.395 9049 Z= 0.336 Chirality : 0.040 0.138 930 Planarity : 0.006 0.043 1111 Dihedral : 16.953 112.314 2272 Min Nonbonded Distance : 1.092 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.39 % Allowed : 19.28 % Favored : 78.33 % 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: 1.48 (0.30), residues: 768 helix: 1.09 (0.22), residues: 517 sheet: None (None), residues: 0 loop : 1.07 (0.43), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 151 TYR 0.013 0.002 TYR C 81 PHE 0.011 0.001 PHE C 134 TRP 0.011 0.001 TRP C 190 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 ( 6640) covalent geometry : angle 0.58718 / 0.34 ( 9049) hydrogen bonds : bond 0.14641 / 10.11 ( 427) hydrogen bonds : angle 6.74892 / 4.75 ( 1272) Misc. bond : bond 0.00062 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.250 Fit side-chains REVERT: A 76 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8667 (tp) REVERT: A 114 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8075 (mm) REVERT: A 183 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6884 (mttp) REVERT: B 183 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6941 (mttp) REVERT: C 76 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8639 (tp) REVERT: C 183 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6899 (mttp) outliers start: 16 outliers final: 8 residues processed: 69 average time/residue: 0.4034 time to fit residues: 29.8075 Evaluate side-chains 70 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.106865 restraints weight = 6051.525| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 0.87 r_work: 0.2977 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6643 Z= 0.196 Angle : 0.585 5.950 9049 Z= 0.296 Chirality : 0.042 0.167 930 Planarity : 0.006 0.048 1111 Dihedral : 11.776 112.314 909 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.74 % Allowed : 15.70 % Favored : 80.57 % 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: 1.91 (0.29), residues: 768 helix: 1.56 (0.20), residues: 523 sheet: None (None), residues: 0 loop : 0.85 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 176 TYR 0.011 0.002 TYR A 101 PHE 0.010 0.002 PHE C 144 TRP 0.008 0.002 TRP C 190 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 ( 6640) covalent geometry : angle 0.58546 / 0.30 ( 9049) hydrogen bonds : bond 0.05378 / 3.62 ( 427) hydrogen bonds : angle 4.72849 / 3.43 ( 1272) Misc. bond : bond 0.00016 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.256 Fit side-chains REVERT: A 183 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6809 (mttp) REVERT: B 183 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6866 (mttp) REVERT: C 183 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6858 (mttp) outliers start: 25 outliers final: 17 residues processed: 81 average time/residue: 0.4457 time to fit residues: 38.4598 Evaluate side-chains 76 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.0170 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.0030 chunk 18 optimal weight: 0.9990 overall best weight: 0.7632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.125996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.110457 restraints weight = 6028.403| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 0.92 r_work: 0.3158 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6643 Z= 0.146 Angle : 0.529 6.001 9049 Z= 0.264 Chirality : 0.040 0.179 930 Planarity : 0.005 0.047 1111 Dihedral : 11.545 111.595 902 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.33 % Allowed : 16.44 % Favored : 79.22 % 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: 2.37 (0.29), residues: 768 helix: 1.94 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.94 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 176 TYR 0.008 0.001 TYR B 22 PHE 0.011 0.001 PHE C 134 TRP 0.008 0.001 TRP A 42 HIS 0.002 0.000 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6640) covalent geometry : angle 0.52918 / 0.26 ( 9049) hydrogen bonds : bond 0.04798 / 3.25 ( 427) hydrogen bonds : angle 4.55457 / 3.31 ( 1272) Misc. bond : bond 0.00020 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.264 Fit side-chains REVERT: A 183 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6712 (mttp) REVERT: B 183 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6759 (mttp) REVERT: C 183 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6752 (mttp) outliers start: 29 outliers final: 19 residues processed: 87 average time/residue: 0.3944 time to fit residues: 36.7338 Evaluate side-chains 79 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 59 optimal weight: 2.9990 chunk 50 optimal weight: 0.0010 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.110750 restraints weight = 6107.933| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 0.93 r_work: 0.3161 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6643 Z= 0.140 Angle : 0.524 6.025 9049 Z= 0.260 Chirality : 0.039 0.161 930 Planarity : 0.005 0.047 1111 Dihedral : 11.496 111.130 902 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.89 % Allowed : 17.49 % Favored : 78.62 % 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: 2.55 (0.29), residues: 768 helix: 2.11 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.94 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.009 0.001 TYR B 22 PHE 0.011 0.001 PHE C 134 TRP 0.008 0.001 TRP C 190 HIS 0.002 0.000 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 6640) covalent geometry : angle 0.52410 / 0.26 ( 9049) hydrogen bonds : bond 0.04638 / 3.13 ( 427) hydrogen bonds : angle 4.45902 / 3.24 ( 1272) Misc. bond : bond 0.00013 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.268 Fit side-chains REVERT: A 183 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6676 (mttp) REVERT: B 183 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6745 (mttp) REVERT: C 183 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6709 (mttp) outliers start: 26 outliers final: 18 residues processed: 83 average time/residue: 0.4222 time to fit residues: 37.5240 Evaluate side-chains 77 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.126476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111661 restraints weight = 6084.877| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 0.86 r_work: 0.3231 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6643 Z= 0.164 Angle : 0.543 6.146 9049 Z= 0.270 Chirality : 0.041 0.179 930 Planarity : 0.005 0.048 1111 Dihedral : 11.505 110.617 902 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.33 % Allowed : 17.34 % Favored : 78.33 % 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: 2.46 (0.29), residues: 768 helix: 2.04 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.89 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.011 0.002 TYR B 22 PHE 0.010 0.001 PHE A 134 TRP 0.008 0.001 TRP B 138 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 6640) covalent geometry : angle 0.54272 / 0.27 ( 9049) hydrogen bonds : bond 0.04850 / 3.28 ( 427) hydrogen bonds : angle 4.45603 / 3.23 ( 1272) Misc. bond : bond 0.00012 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.259 Fit side-chains REVERT: A 183 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6761 (mttp) REVERT: B 183 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6810 (mttp) REVERT: C 183 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6779 (mttp) outliers start: 29 outliers final: 18 residues processed: 87 average time/residue: 0.4776 time to fit residues: 44.1337 Evaluate side-chains 82 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115383 restraints weight = 6035.079| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 0.91 r_work: 0.3320 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6643 Z= 0.145 Angle : 0.530 6.049 9049 Z= 0.263 Chirality : 0.039 0.169 930 Planarity : 0.005 0.047 1111 Dihedral : 11.460 110.465 902 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.48 % Allowed : 17.34 % Favored : 78.18 % 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: 2.52 (0.29), residues: 768 helix: 2.10 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.90 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.009 0.001 TYR B 22 PHE 0.011 0.001 PHE A 134 TRP 0.009 0.001 TRP A 190 HIS 0.002 0.000 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6640) covalent geometry : angle 0.53046 / 0.26 ( 9049) hydrogen bonds : bond 0.04670 / 3.16 ( 427) hydrogen bonds : angle 4.41728 / 3.20 ( 1272) Misc. bond : bond 0.00012 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.257 Fit side-chains REVERT: B 183 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6765 (mttp) REVERT: C 183 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6732 (mttp) outliers start: 30 outliers final: 21 residues processed: 85 average time/residue: 0.4606 time to fit residues: 41.7009 Evaluate side-chains 82 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.129966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115011 restraints weight = 5990.406| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 0.91 r_work: 0.3296 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6643 Z= 0.152 Angle : 0.538 6.085 9049 Z= 0.266 Chirality : 0.040 0.171 930 Planarity : 0.005 0.047 1111 Dihedral : 11.260 109.984 898 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.19 % Allowed : 17.49 % Favored : 78.33 % 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: 2.50 (0.29), residues: 768 helix: 2.08 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.89 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.010 0.002 TYR B 22 PHE 0.010 0.001 PHE A 134 TRP 0.008 0.001 TRP A 190 HIS 0.002 0.000 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 6640) covalent geometry : angle 0.53839 / 0.27 ( 9049) hydrogen bonds : bond 0.04730 / 3.20 ( 427) hydrogen bonds : angle 4.41361 / 3.20 ( 1272) Misc. bond : bond 0.00012 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.276 Fit side-chains REVERT: B 183 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6761 (mttp) REVERT: C 183 LYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6750 (mttp) outliers start: 28 outliers final: 21 residues processed: 87 average time/residue: 0.4925 time to fit residues: 45.4704 Evaluate side-chains 83 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 19 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.136210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122077 restraints weight = 5767.201| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 0.86 r_work: 0.3388 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6643 Z= 0.134 Angle : 0.528 6.023 9049 Z= 0.260 Chirality : 0.039 0.165 930 Planarity : 0.005 0.047 1111 Dihedral : 11.207 109.861 898 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.59 % Allowed : 18.24 % Favored : 78.18 % 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: 2.59 (0.29), residues: 768 helix: 2.14 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.92 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 186 TYR 0.008 0.001 TYR B 22 PHE 0.011 0.001 PHE A 134 TRP 0.008 0.001 TRP C 190 HIS 0.001 0.000 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 6640) covalent geometry : angle 0.52754 / 0.26 ( 9049) hydrogen bonds : bond 0.04535 / 3.07 ( 427) hydrogen bonds : angle 4.38497 / 3.18 ( 1272) Misc. bond : bond 0.00012 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.270 Fit side-chains REVERT: B 183 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6862 (mttp) REVERT: C 183 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6691 (mttp) outliers start: 24 outliers final: 21 residues processed: 85 average time/residue: 0.4431 time to fit residues: 40.2560 Evaluate side-chains 79 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 26 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 chunk 70 optimal weight: 0.0770 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120400 restraints weight = 5947.719| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 0.92 r_work: 0.3408 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6643 Z= 0.122 Angle : 0.511 5.959 9049 Z= 0.252 Chirality : 0.038 0.160 930 Planarity : 0.005 0.046 1111 Dihedral : 11.158 109.513 898 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.74 % Allowed : 18.09 % Favored : 78.18 % 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: 2.70 (0.29), residues: 768 helix: 2.24 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.94 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 186 TYR 0.008 0.001 TYR B 22 PHE 0.011 0.001 PHE A 134 TRP 0.007 0.001 TRP C 190 HIS 0.001 0.000 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 6640) covalent geometry : angle 0.51082 / 0.25 ( 9049) hydrogen bonds : bond 0.04351 / 2.95 ( 427) hydrogen bonds : angle 4.34532 / 3.15 ( 1272) Misc. bond : bond 0.00014 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.272 Fit side-chains REVERT: B 170 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7744 (tpt) REVERT: B 183 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6657 (mttp) REVERT: C 183 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.6574 (mttp) outliers start: 25 outliers final: 21 residues processed: 81 average time/residue: 0.4640 time to fit residues: 40.0318 Evaluate side-chains 84 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 25 optimal weight: 0.0020 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.123973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.108263 restraints weight = 5858.492| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 0.86 r_work: 0.3364 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6643 Z= 0.163 Angle : 0.551 6.076 9049 Z= 0.274 Chirality : 0.041 0.173 930 Planarity : 0.005 0.046 1111 Dihedral : 11.157 108.318 898 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.74 % Allowed : 17.34 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.29), residues: 768 helix: 2.08 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.95 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.011 0.002 TYR B 22 PHE 0.010 0.001 PHE C 134 TRP 0.009 0.001 TRP A 190 HIS 0.002 0.000 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 6640) covalent geometry : angle 0.55112 / 0.27 ( 9049) hydrogen bonds : bond 0.04795 / 3.25 ( 427) hydrogen bonds : angle 4.39279 / 3.18 ( 1272) Misc. bond : bond 0.00011 / 0.01 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.299 Fit side-chains REVERT: B 170 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7850 (tpt) REVERT: B 183 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6845 (mttp) REVERT: C 183 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6741 (mttp) outliers start: 25 outliers final: 18 residues processed: 85 average time/residue: 0.4541 time to fit residues: 41.1582 Evaluate side-chains 82 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain B residue 33 CYS Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 183 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.0030 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.137059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.122609 restraints weight = 5706.916| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 0.87 r_work: 0.3393 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6643 Z= 0.134 Angle : 0.526 5.961 9049 Z= 0.260 Chirality : 0.039 0.166 930 Planarity : 0.005 0.046 1111 Dihedral : 11.168 108.857 898 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.44 % Allowed : 17.64 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.29), residues: 768 helix: 2.18 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.96 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 176 TYR 0.009 0.001 TYR B 22 PHE 0.011 0.001 PHE A 134 TRP 0.009 0.001 TRP A 190 HIS 0.001 0.000 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 6640) covalent geometry : angle 0.52622 / 0.26 ( 9049) hydrogen bonds : bond 0.04507 / 3.05 ( 427) hydrogen bonds : angle 4.36426 / 3.17 ( 1272) Misc. bond : bond 0.00014 / 0.01 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2617.73 seconds wall clock time: 45 minutes 42.86 seconds (2742.86 seconds total)