Starting phenix.real_space_refine on Wed Sep 17 06:46:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zaq_39884/09_2025/8zaq_39884_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zaq_39884/09_2025/8zaq_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_39884/09_2025/8zaq_39884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zaq_39884/09_2025/8zaq_39884.map" model { file = "/net/cci-nas-00/data/ceres_data/8zaq_39884/09_2025/8zaq_39884_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zaq_39884/09_2025/8zaq_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-2.0-5805/lib/python3.9/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, 29 Unusual residues: {' K': 8, 'RET': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 29 Unusual residues: {' K': 8, 'RET': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 29 Unusual residues: {' K': 8, 'RET': 1} Classifications: {'undetermined': 9} Link IDs: {None: 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: 1.92, per 1000 atoms: 0.30 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: 0.60 Conformation dependent library (CDL) restraints added in 353.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.19 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: 1.04 Time building geometry restraints manager: 0.79 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 2.850 nonbonded pdb=" K K C 305 " pdb=" O HOH C 409 " model vdw 1.094 2.850 nonbonded pdb=" K K A 305 " pdb=" O HOH A 409 " model vdw 1.098 2.850 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: 25.700 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.280 Find NCS groups from input model: 0.140 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:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 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 aren 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 covalent geometry : bond 0.00335 ( 6640) covalent geometry : angle 0.58718 ( 9049) hydrogen bonds : bond 0.14641 ( 427) hydrogen bonds : angle 6.74892 ( 1272) Misc. bond : bond 0.00062 ( 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 : 0.277 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: 0.6898 (mttp) outliers start: 16 outliers final: 8 residues processed: 69 average time/residue: 0.4893 time to fit residues: 35.9927 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 : 0.279 ------------------------------------------------------------------------------- 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: 0.3980 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: 0.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.106433 restraints weight = 6365.814| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 0.95 r_work: 0.3184 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6643 Z= 0.192 Angle : 0.580 5.926 9049 Z= 0.294 Chirality : 0.042 0.171 930 Planarity : 0.006 0.048 1111 Dihedral : 11.811 112.291 909 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.74 % Allowed : 16.14 % Favored : 80.12 % 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 aren not related in a simple way. whole: 1.97 (0.29), residues: 768 helix: 1.60 (0.20), residues: 523 sheet: None (None), residues: 0 loop : 0.88 (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 B 22 PHE 0.010 0.002 PHE C 144 TRP 0.008 0.001 TRP B 138 HIS 0.002 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 6640) covalent geometry : angle 0.58009 ( 9049) hydrogen bonds : bond 0.05355 ( 427) hydrogen bonds : angle 4.70660 ( 1272) Misc. bond : bond 0.00021 ( 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 87 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.299 Fit side-chains REVERT: A 183 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6790 (mttp) REVERT: B 183 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6876 (mttp) REVERT: C 183 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6824 (mttp) outliers start: 25 outliers final: 15 residues processed: 83 average time/residue: 0.4959 time to fit residues: 43.8448 Evaluate side-chains 76 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 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 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: 0.0470 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.105238 restraints weight = 6343.940| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 0.91 r_work: 0.3253 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1012 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= 0.158 Angle : 0.536 6.030 9049 Z= 0.269 Chirality : 0.040 0.184 930 Planarity : 0.005 0.048 1111 Dihedral : 11.546 111.241 902 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.89 % Allowed : 17.19 % 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 aren not related in a simple way. whole: 2.38 (0.29), residues: 768 helix: 1.98 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.89 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.009 0.002 TYR B 22 PHE 0.011 0.001 PHE C 134 TRP 0.011 0.001 TRP C 190 HIS 0.002 0.000 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6640) covalent geometry : angle 0.53591 ( 9049) hydrogen bonds : bond 0.04913 ( 427) hydrogen bonds : angle 4.55903 ( 1272) Misc. bond : bond 0.00014 ( 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 92 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.318 Fit side-chains REVERT: A 183 LYS cc_start: 0.6933 (OUTLIER) cc_final: 0.6692 (mttp) REVERT: B 183 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6747 (mttp) REVERT: C 171 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7611 (ttp-170) REVERT: C 183 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6717 (mttp) outliers start: 26 outliers final: 14 residues processed: 87 average time/residue: 0.4337 time to fit residues: 40.1542 Evaluate side-chains 78 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 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 33 CYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 171 ARG 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: 0.8980 chunk 50 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.122892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.108340 restraints weight = 6430.167| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 0.96 r_work: 0.3155 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1116 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= 0.139 Angle : 0.521 5.984 9049 Z= 0.260 Chirality : 0.039 0.163 930 Planarity : 0.005 0.048 1111 Dihedral : 11.502 110.843 902 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.04 % Allowed : 17.49 % Favored : 78.48 % 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 aren not related in a simple way. whole: 2.56 (0.29), residues: 768 helix: 2.13 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.88 (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 C 134 TRP 0.008 0.001 TRP C 190 HIS 0.002 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6640) covalent geometry : angle 0.52141 ( 9049) hydrogen bonds : bond 0.04661 ( 427) hydrogen bonds : angle 4.45001 ( 1272) Misc. bond : bond 0.00014 ( 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 92 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.234 Fit side-chains REVERT: A 183 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6702 (mttp) REVERT: B 183 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6777 (mttp) REVERT: C 183 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6721 (mttp) outliers start: 27 outliers final: 15 residues processed: 89 average time/residue: 0.4293 time to fit residues: 40.8163 Evaluate side-chains 78 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111137 restraints weight = 6354.809| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 0.93 r_work: 0.3286 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1156 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 : 0.529 5.971 9049 Z= 0.263 Chirality : 0.039 0.171 930 Planarity : 0.005 0.048 1111 Dihedral : 11.479 110.519 902 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.63 % Allowed : 17.49 % Favored : 77.88 % 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 aren not related in a simple way. whole: 2.59 (0.29), residues: 768 helix: 2.15 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.91 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.010 0.001 TYR B 22 PHE 0.010 0.001 PHE A 134 TRP 0.007 0.001 TRP C 190 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6640) covalent geometry : angle 0.52945 ( 9049) hydrogen bonds : bond 0.04692 ( 427) hydrogen bonds : angle 4.41852 ( 1272) Misc. bond : bond 0.00013 ( 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: 31 poor density : 61 time to evaluate : 0.221 Fit side-chains REVERT: A 183 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6705 (mttp) REVERT: B 183 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6803 (mttp) REVERT: C 183 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6734 (mttp) outliers start: 31 outliers final: 15 residues processed: 87 average time/residue: 0.4924 time to fit residues: 45.4643 Evaluate side-chains 76 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 5 ASP 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 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 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: 0.9980 chunk 65 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.124097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.110041 restraints weight = 6348.533| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 0.93 r_work: 0.3316 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6643 Z= 0.159 Angle : 0.542 6.060 9049 Z= 0.270 Chirality : 0.040 0.172 930 Planarity : 0.005 0.048 1111 Dihedral : 11.461 110.135 902 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.89 % Allowed : 17.79 % 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 aren 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 0.011 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 covalent geometry : bond 0.00360 ( 6640) covalent geometry : angle 0.54163 ( 9049) hydrogen bonds : bond 0.04817 ( 427) hydrogen bonds : angle 4.42742 ( 1272) Misc. bond : bond 0.00015 ( 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 89 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.307 Fit side-chains REVERT: A 183 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6849 (mttp) REVERT: B 183 LYS cc_start: 0.7052 (OUTLIER) cc_final: 0.6784 (mttp) REVERT: C 183 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6715 (mttp) outliers start: 26 outliers final: 16 residues processed: 87 average time/residue: 0.4970 time to fit residues: 45.9259 Evaluate side-chains 80 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 5 ASP 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 33 CYS Chi-restraints excluded: chain C residue 107 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 45 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 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: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.110144 restraints weight = 6263.196| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 0.86 r_work: 0.3307 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1192 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= 0.166 Angle : 0.552 6.221 9049 Z= 0.274 Chirality : 0.041 0.176 930 Planarity : 0.005 0.048 1111 Dihedral : 11.448 109.934 902 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.59 % Allowed : 18.09 % 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 aren not related in a simple way. whole: 2.46 (0.29), residues: 768 helix: 2.06 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.85 (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 0.009 0.001 TRP A 190 HIS 0.002 0.001 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 6640) covalent geometry : angle 0.55197 ( 9049) hydrogen bonds : bond 0.04886 ( 427) hydrogen bonds : angle 4.44590 ( 1272) Misc. bond : bond 0.00010 ( 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 88 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.273 Fit side-chains REVERT: A 183 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6799 (mttp) REVERT: B 183 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6906 (mttp) REVERT: C 183 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6696 (mttp) outliers start: 24 outliers final: 17 residues processed: 84 average time/residue: 0.5001 time to fit residues: 44.6907 Evaluate side-chains 81 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 5 ASP 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 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: 0.6980 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 19 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.0570 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116782 restraints weight = 6115.982| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 0.92 r_work: 0.3369 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1318 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= 0.121 Angle : 0.512 5.841 9049 Z= 0.253 Chirality : 0.038 0.159 930 Planarity : 0.005 0.047 1111 Dihedral : 11.371 110.108 902 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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 aren not related in a simple way. whole: 2.71 (0.29), residues: 768 helix: 2.27 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.88 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 186 TYR 0.008 0.001 TYR A 45 PHE 0.011 0.001 PHE A 134 TRP 0.009 0.001 TRP A 42 HIS 0.001 0.000 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6640) covalent geometry : angle 0.51178 ( 9049) hydrogen bonds : bond 0.04374 ( 427) hydrogen bonds : angle 4.35237 ( 1272) Misc. bond : bond 0.00016 ( 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 91 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.281 Fit side-chains REVERT: B 183 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6778 (mttp) REVERT: C 183 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6777 (mttp) outliers start: 24 outliers final: 18 residues processed: 87 average time/residue: 0.4840 time to fit residues: 44.8527 Evaluate side-chains 79 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 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 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 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: 0.8980 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.119737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.105220 restraints weight = 6294.247| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 0.90 r_work: 0.3346 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1310 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= 0.153 Angle : 0.542 6.180 9049 Z= 0.269 Chirality : 0.040 0.169 930 Planarity : 0.005 0.047 1111 Dihedral : 11.149 108.982 898 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.14 % Allowed : 18.54 % 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 aren not related in a simple way. whole: 2.60 (0.29), residues: 768 helix: 2.17 (0.21), residues: 523 sheet: None (None), residues: 0 loop : 0.91 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 186 TYR 0.010 0.001 TYR C 22 PHE 0.010 0.001 PHE C 134 TRP 0.008 0.001 TRP B 190 HIS 0.002 0.000 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6640) covalent geometry : angle 0.54227 ( 9049) hydrogen bonds : bond 0.04711 ( 427) hydrogen bonds : angle 4.37820 ( 1272) Misc. bond : bond 0.00010 ( 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 82 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.266 Fit side-chains REVERT: B 183 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6843 (mttp) REVERT: C 183 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6789 (mttp) outliers start: 21 outliers final: 15 residues processed: 80 average time/residue: 0.5051 time to fit residues: 42.9256 Evaluate side-chains 76 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 110 THR 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 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 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: 1.9990 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.120612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.106307 restraints weight = 6148.027| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 0.89 r_work: 0.3259 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1350 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 : 0.537 5.944 9049 Z= 0.267 Chirality : 0.040 0.171 930 Planarity : 0.005 0.047 1111 Dihedral : 11.164 108.914 898 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.14 % Allowed : 18.39 % Favored : 78.48 % 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 aren not related in a simple way. whole: 2.60 (0.29), residues: 768 helix: 2.15 (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 C 176 TYR 0.010 0.001 TYR B 22 PHE 0.025 0.001 PHE A 144 TRP 0.009 0.001 TRP B 190 HIS 0.002 0.000 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6640) covalent geometry : angle 0.53695 ( 9049) hydrogen bonds : bond 0.04737 ( 427) hydrogen bonds : angle 4.39351 ( 1272) Misc. bond : bond 0.00010 ( 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 82 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.285 Fit side-chains REVERT: B 170 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7865 (tpt) REVERT: B 183 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6858 (mttp) REVERT: C 183 LYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6805 (mttp) outliers start: 21 outliers final: 17 residues processed: 79 average time/residue: 0.5131 time to fit residues: 43.0752 Evaluate side-chains 80 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 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 70 SER 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 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 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: 0.9980 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.120787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.106493 restraints weight = 6167.758| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 0.89 r_work: 0.3333 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 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= 0.147 Angle : 0.534 5.963 9049 Z= 0.266 Chirality : 0.040 0.169 930 Planarity : 0.005 0.047 1111 Dihedral : 11.160 108.728 898 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.14 % Allowed : 18.39 % Favored : 78.48 % 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 aren not related in a simple way. whole: 2.61 (0.29), residues: 768 helix: 2.16 (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 C 186 TYR 0.010 0.001 TYR B 22 PHE 0.024 0.001 PHE A 144 TRP 0.009 0.001 TRP B 190 HIS 0.002 0.000 HIS C 225 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6640) covalent geometry : angle 0.53367 ( 9049) hydrogen bonds : bond 0.04705 ( 427) hydrogen bonds : angle 4.38952 ( 1272) Misc. bond : bond 0.00010 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2762.14 seconds wall clock time: 48 minutes 8.36 seconds (2888.36 seconds total)