Starting phenix.real_space_refine on Thu Jul 2 03:03:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxp_36708/07_2026/8jxp_36708_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxp_36708/07_2026/8jxp_36708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxp_36708/07_2026/8jxp_36708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxp_36708/07_2026/8jxp_36708.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxp_36708/07_2026/8jxp_36708_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxp_36708/07_2026/8jxp_36708_neut.cif" } resolution = 2.7 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= 0.009 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 18 8.98 5 S 42 5.16 5 C 4176 2.51 5 N 954 2.21 5 O 1104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.00s 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: 6294 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2069 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 20 Ad-hoc single atom residues: {' K': 6} Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 518 SG CYS A 72 33.958 19.202 56.026 1.00 30.00 S Restraints were copied for chains: B, C Time building chain proxies: 1.41, per 1000 atoms: 0.22 Number of scatterers: 6294 At special positions: 0 Unit cell: (74.2, 72.1, 90.3, 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 18 19.00 S 42 16.00 O 1104 8.00 N 954 7.00 C 4176 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: 0.38 Conformation dependent library (CDL) restraints added in 327.9 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 81.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 Processing helix chain 'A' and resid 17 through 45 Processing helix chain 'A' and resid 59 through 62 Processing helix chain 'A' and resid 63 through 89 Processing helix chain 'A' and resid 103 through 120 removed outlier: 4.484A pdb=" N ILE A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 124 through 145 removed outlier: 3.830A pdb=" N VAL A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 174 removed outlier: 3.626A pdb=" N TYR A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 152 " --> pdb=" O PRO A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.826A pdb=" N TRP A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 removed outlier: 3.587A pdb=" N PHE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Proline residue: A 202 - end of helix removed outlier: 3.533A pdb=" N TRP A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 216 through 231 removed outlier: 3.534A pdb=" N ILE A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 263 Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 17 through 45 Processing helix chain 'B' and resid 59 through 62 Processing helix chain 'B' and resid 63 through 89 Processing helix chain 'B' and resid 103 through 120 removed outlier: 4.484A pdb=" N ILE B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 124 through 145 removed outlier: 3.830A pdb=" N VAL B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 174 removed outlier: 3.626A pdb=" N TYR B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.826A pdb=" N TRP B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 205 removed outlier: 3.587A pdb=" N PHE B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Proline residue: B 202 - end of helix removed outlier: 3.533A pdb=" N TRP B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 216 through 231 removed outlier: 3.534A pdb=" N ILE B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 263 Processing helix chain 'C' and resid 8 through 12 Processing helix chain 'C' and resid 17 through 45 Processing helix chain 'C' and resid 59 through 62 Processing helix chain 'C' and resid 63 through 89 Processing helix chain 'C' and resid 103 through 120 removed outlier: 4.483A pdb=" N ILE C 107 " --> pdb=" O SER C 103 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 124 through 145 removed outlier: 3.830A pdb=" N VAL C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 174 removed outlier: 3.626A pdb=" N TYR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 152 " --> pdb=" O PRO C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 196 removed outlier: 3.826A pdb=" N TRP C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TYR C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 205 removed outlier: 3.587A pdb=" N PHE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Proline residue: C 202 - end of helix removed outlier: 3.533A pdb=" N TRP C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 216 through 231 removed outlier: 3.534A pdb=" N ILE C 226 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 263 456 hydrogen bonds defined for protein. 1341 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: 0.85 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 981 1.32 - 1.44: 1938 1.44 - 1.56: 3492 1.56 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 6465 Sorted by residual: bond pdb=" CA LEU B 192 " pdb=" C LEU B 192 " ideal model delta sigma weight residual 1.524 1.472 0.053 1.24e-02 6.50e+03 1.80e+01 bond pdb=" CA LEU C 192 " pdb=" C LEU C 192 " ideal model delta sigma weight residual 1.524 1.472 0.053 1.24e-02 6.50e+03 1.80e+01 bond pdb=" CA LEU A 192 " pdb=" C LEU A 192 " ideal model delta sigma weight residual 1.524 1.472 0.053 1.24e-02 6.50e+03 1.80e+01 bond pdb=" C ASP C 82 " pdb=" O ASP C 82 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.17e-02 7.31e+03 1.34e+01 bond pdb=" C ASP A 82 " pdb=" O ASP A 82 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.17e-02 7.31e+03 1.33e+01 ... (remaining 6460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 8319 2.41 - 4.83: 409 4.83 - 7.24: 47 7.24 - 9.65: 39 9.65 - 12.06: 12 Bond angle restraints: 8826 Sorted by residual: angle pdb=" N ALA A 137 " pdb=" CA ALA A 137 " pdb=" C ALA A 137 " ideal model delta sigma weight residual 113.41 101.83 11.58 1.22e+00 6.72e-01 9.01e+01 angle pdb=" N ALA C 137 " pdb=" CA ALA C 137 " pdb=" C ALA C 137 " ideal model delta sigma weight residual 113.41 101.86 11.55 1.22e+00 6.72e-01 8.96e+01 angle pdb=" N ALA B 137 " pdb=" CA ALA B 137 " pdb=" C ALA B 137 " ideal model delta sigma weight residual 113.41 101.87 11.54 1.22e+00 6.72e-01 8.95e+01 angle pdb=" N LEU B 192 " pdb=" CA LEU B 192 " pdb=" C LEU B 192 " ideal model delta sigma weight residual 110.97 100.70 10.27 1.09e+00 8.42e-01 8.87e+01 angle pdb=" N LEU A 192 " pdb=" CA LEU A 192 " pdb=" C LEU A 192 " ideal model delta sigma weight residual 110.97 100.71 10.26 1.09e+00 8.42e-01 8.87e+01 ... (remaining 8821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 2928 17.06 - 34.11: 390 34.11 - 51.17: 216 51.17 - 68.23: 96 68.23 - 85.28: 15 Dihedral angle restraints: 3645 sinusoidal: 1371 harmonic: 2274 Sorted by residual: dihedral pdb=" C ALA B 147 " pdb=" N ALA B 147 " pdb=" CA ALA B 147 " pdb=" CB ALA B 147 " ideal model delta harmonic sigma weight residual -122.60 -134.54 11.94 0 2.50e+00 1.60e-01 2.28e+01 dihedral pdb=" C ALA A 147 " pdb=" N ALA A 147 " pdb=" CA ALA A 147 " pdb=" CB ALA A 147 " ideal model delta harmonic sigma weight residual -122.60 -134.53 11.93 0 2.50e+00 1.60e-01 2.28e+01 dihedral pdb=" C ALA C 147 " pdb=" N ALA C 147 " pdb=" CA ALA C 147 " pdb=" CB ALA C 147 " ideal model delta harmonic sigma weight residual -122.60 -134.50 11.90 0 2.50e+00 1.60e-01 2.27e+01 ... (remaining 3642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 804 0.110 - 0.221: 114 0.221 - 0.331: 24 0.331 - 0.441: 6 0.441 - 0.551: 6 Chirality restraints: 954 Sorted by residual: chirality pdb=" CA ALA A 147 " pdb=" N ALA A 147 " pdb=" C ALA A 147 " pdb=" CB ALA A 147 " both_signs ideal model delta sigma weight residual False 2.48 1.93 0.55 2.00e-01 2.50e+01 7.60e+00 chirality pdb=" CA ALA B 147 " pdb=" N ALA B 147 " pdb=" C ALA B 147 " pdb=" CB ALA B 147 " both_signs ideal model delta sigma weight residual False 2.48 1.93 0.55 2.00e-01 2.50e+01 7.59e+00 chirality pdb=" CA ALA C 147 " pdb=" N ALA C 147 " pdb=" C ALA C 147 " pdb=" CB ALA C 147 " both_signs ideal model delta sigma weight residual False 2.48 1.94 0.55 2.00e-01 2.50e+01 7.53e+00 ... (remaining 951 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 109 " -0.113 5.00e-02 4.00e+02 1.65e-01 4.34e+01 pdb=" N PRO A 110 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " -0.096 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 109 " -0.113 5.00e-02 4.00e+02 1.65e-01 4.34e+01 pdb=" N PRO B 110 " 0.284 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " -0.096 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 109 " 0.113 5.00e-02 4.00e+02 1.65e-01 4.34e+01 pdb=" N PRO C 110 " -0.284 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " 0.096 5.00e-02 4.00e+02 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.34: 12 2.34 - 3.04: 4128 3.04 - 3.74: 12479 3.74 - 4.44: 20818 4.44 - 5.14: 31787 Nonbonded interactions: 69224 Sorted by model distance: nonbonded pdb=" CG MET A 239 " pdb=" K K A 401 " model vdw 1.644 3.990 nonbonded pdb=" CG MET C 239 " pdb=" K K C 401 " model vdw 1.644 3.990 nonbonded pdb=" CG MET B 239 " pdb=" K K B 401 " model vdw 1.645 3.990 nonbonded pdb=" CB MET A 239 " pdb=" K K A 401 " model vdw 1.890 3.990 nonbonded pdb=" CB MET B 239 " pdb=" K K B 401 " model vdw 1.890 3.990 ... (remaining 69219 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 20.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.710 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.009 0.053 6468 Z= 0.645 Angle : 1.325 12.064 8826 Z= 0.904 Chirality : 0.095 0.551 954 Planarity : 0.016 0.165 1095 Dihedral : 22.329 85.284 2193 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 1.92 % Allowed : 6.92 % Favored : 91.15 % Rotamer: Outliers : 24.41 % Allowed : 13.15 % Favored : 62.44 % Cbeta Deviations : 0.83 % 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: -2.49 (0.26), residues: 780 helix: -1.57 (0.17), residues: 555 sheet: None (None), residues: 0 loop : -1.35 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 176 TYR 0.010 0.002 TYR A 102 PHE 0.037 0.003 PHE A 143 TRP 0.011 0.002 TRP A 219 HIS 0.005 0.002 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00868 / 0.64 ( 6465) covalent geometry : angle 1.32543 / 0.90 ( 8826) hydrogen bonds : bond 0.16354 / 11.10 ( 456) hydrogen bonds : angle 6.48951 / 4.68 ( 1341) Misc. bond : bond 0.05116 / 2.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 99 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7067 (mt) REVERT: A 203 LEU cc_start: 0.8053 (mt) cc_final: 0.7844 (tp) REVERT: B 126 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7087 (mt) REVERT: B 203 LEU cc_start: 0.8043 (mt) cc_final: 0.7811 (tp) REVERT: C 126 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7137 (mt) REVERT: C 203 LEU cc_start: 0.8047 (mt) cc_final: 0.7818 (tp) outliers start: 156 outliers final: 25 residues processed: 228 average time/residue: 0.3751 time to fit residues: 91.0005 Evaluate side-chains 91 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 TYR Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 202 PRO Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 5 CYS Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 149 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 202 PRO Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 5 CYS Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 202 PRO Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 261 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 0.0770 chunk 74 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN A 98 ASN A 99 GLN A 210 HIS B 99 GLN B 210 HIS C 98 ASN C 99 GLN C 175 GLN C 210 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.166721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.140574 restraints weight = 5912.385| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.48 r_work: 0.3771 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6468 Z= 0.152 Angle : 0.628 8.275 8826 Z= 0.326 Chirality : 0.041 0.131 954 Planarity : 0.007 0.080 1095 Dihedral : 10.438 67.409 929 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.77 % Allowed : 3.08 % Favored : 96.15 % Rotamer: Outliers : 7.04 % Allowed : 19.09 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.29), residues: 780 helix: 1.34 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -0.48 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 243 TYR 0.015 0.002 TYR B 86 PHE 0.010 0.001 PHE B 195 TRP 0.012 0.001 TRP A 198 HIS 0.004 0.002 HIS A 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 6465) covalent geometry : angle 0.62766 / 0.33 ( 8826) hydrogen bonds : bond 0.04692 / 3.26 ( 456) hydrogen bonds : angle 4.08916 / 2.99 ( 1341) Misc. bond : bond 0.00057 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 54 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7496 (pt0) REVERT: A 11 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.6795 (mp10) REVERT: A 13 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: A 194 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7728 (t80) REVERT: A 203 LEU cc_start: 0.8134 (mt) cc_final: 0.7787 (tp) REVERT: B 6 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7506 (pt0) REVERT: B 13 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7335 (mt-10) REVERT: B 194 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7675 (t80) REVERT: B 203 LEU cc_start: 0.8088 (mt) cc_final: 0.7768 (tp) REVERT: C 6 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7524 (pt0) REVERT: C 13 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: C 132 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7644 (mp) REVERT: C 194 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7676 (t80) REVERT: C 203 LEU cc_start: 0.8158 (mt) cc_final: 0.7803 (tp) REVERT: C 260 LYS cc_start: 0.2972 (OUTLIER) cc_final: 0.2763 (mppt) outliers start: 45 outliers final: 21 residues processed: 92 average time/residue: 0.3776 time to fit residues: 37.0887 Evaluate side-chains 75 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 45 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 261 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 73 optimal weight: 0.0050 chunk 69 optimal weight: 0.0980 chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.161124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.136130 restraints weight = 5821.469| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.40 r_work: 0.3734 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6468 Z= 0.122 Angle : 0.536 7.164 8826 Z= 0.271 Chirality : 0.038 0.119 954 Planarity : 0.005 0.061 1095 Dihedral : 9.044 74.025 901 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.85 % Favored : 95.77 % Rotamer: Outliers : 5.48 % Allowed : 22.22 % Favored : 72.30 % 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: 2.73 (0.31), residues: 780 helix: 2.31 (0.21), residues: 594 sheet: None (None), residues: 0 loop : 0.23 (0.50), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.010 0.001 TYR C 86 PHE 0.008 0.001 PHE A 195 TRP 0.013 0.001 TRP C 219 HIS 0.005 0.002 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 6465) covalent geometry : angle 0.53633 / 0.27 ( 8826) hydrogen bonds : bond 0.04241 / 2.94 ( 456) hydrogen bonds : angle 3.81111 / 2.79 ( 1341) Misc. bond : bond 0.00036 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 54 time to evaluate : 0.252 Fit side-chains REVERT: A 6 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7665 (pt0) REVERT: A 200 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7404 (t80) REVERT: B 6 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7626 (pt0) REVERT: B 200 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7427 (t80) outliers start: 35 outliers final: 8 residues processed: 86 average time/residue: 0.3161 time to fit residues: 29.5322 Evaluate side-chains 56 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 194 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.153917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.127964 restraints weight = 5869.170| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.48 r_work: 0.3653 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6468 Z= 0.140 Angle : 0.560 10.852 8826 Z= 0.276 Chirality : 0.039 0.122 954 Planarity : 0.005 0.054 1095 Dihedral : 7.711 87.646 876 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.31 % Favored : 97.31 % Rotamer: Outliers : 3.60 % Allowed : 23.63 % Favored : 72.77 % 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: 3.03 (0.30), residues: 780 helix: 2.59 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 0.33 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 243 TYR 0.014 0.001 TYR A 86 PHE 0.009 0.001 PHE C 195 TRP 0.011 0.001 TRP A 219 HIS 0.004 0.002 HIS B 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6465) covalent geometry : angle 0.55995 / 0.28 ( 8826) hydrogen bonds : bond 0.04377 / 3.04 ( 456) hydrogen bonds : angle 3.76583 / 2.74 ( 1341) Misc. bond : bond 0.00012 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.148 Fit side-chains REVERT: A 6 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7593 (pt0) REVERT: A 200 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7439 (t80) REVERT: B 200 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7474 (t80) REVERT: C 200 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7498 (t80) outliers start: 23 outliers final: 10 residues processed: 67 average time/residue: 0.2871 time to fit residues: 21.2067 Evaluate side-chains 51 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 261 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 64 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.142767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116430 restraints weight = 5720.735| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.30 r_work: 0.3244 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6468 Z= 0.159 Angle : 0.579 11.704 8826 Z= 0.282 Chirality : 0.040 0.123 954 Planarity : 0.005 0.049 1095 Dihedral : 7.031 89.205 870 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.77 % Allowed : 2.56 % Favored : 96.67 % Rotamer: Outliers : 3.60 % Allowed : 24.10 % Favored : 72.30 % 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: 3.07 (0.30), residues: 780 helix: 2.59 (0.20), residues: 576 sheet: None (None), residues: 0 loop : 0.44 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.013 0.002 TYR C 86 PHE 0.009 0.001 PHE C 195 TRP 0.011 0.001 TRP C 219 HIS 0.005 0.002 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 6465) covalent geometry : angle 0.57908 / 0.28 ( 8826) hydrogen bonds : bond 0.04551 / 3.14 ( 456) hydrogen bonds : angle 3.76442 / 2.73 ( 1341) Misc. bond : bond 0.00014 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.275 Fit side-chains REVERT: A 6 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7569 (pt0) REVERT: A 200 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7466 (t80) REVERT: A 203 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8089 (tm) REVERT: B 200 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7442 (t80) REVERT: B 203 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8029 (tm) REVERT: C 200 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7504 (t80) REVERT: C 203 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8080 (tm) outliers start: 23 outliers final: 7 residues processed: 65 average time/residue: 0.2920 time to fit residues: 20.7621 Evaluate side-chains 58 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 261 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.142162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115891 restraints weight = 5702.637| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.30 r_work: 0.3258 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6468 Z= 0.141 Angle : 0.553 11.465 8826 Z= 0.267 Chirality : 0.039 0.122 954 Planarity : 0.005 0.046 1095 Dihedral : 6.852 86.585 870 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.56 % Favored : 97.05 % Rotamer: Outliers : 2.97 % Allowed : 23.94 % Favored : 73.08 % 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: 3.18 (0.30), residues: 780 helix: 2.68 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 0.44 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.011 0.001 TYR C 86 PHE 0.008 0.001 PHE C 195 TRP 0.009 0.001 TRP B 184 HIS 0.006 0.002 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 6465) covalent geometry : angle 0.55328 / 0.27 ( 8826) hydrogen bonds : bond 0.04306 / 2.97 ( 456) hydrogen bonds : angle 3.74895 / 2.72 ( 1341) Misc. bond : bond 0.00011 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.250 Fit side-chains REVERT: A 6 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7569 (pt0) REVERT: A 200 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7515 (t80) REVERT: A 203 LEU cc_start: 0.8430 (mt) cc_final: 0.8110 (tm) REVERT: B 200 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7485 (t80) REVERT: B 203 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8047 (tm) REVERT: C 200 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7535 (t80) REVERT: C 203 LEU cc_start: 0.8441 (mt) cc_final: 0.8085 (tm) outliers start: 19 outliers final: 6 residues processed: 61 average time/residue: 0.3380 time to fit residues: 22.3599 Evaluate side-chains 58 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 261 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 ASN B 49 ASN C 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.142512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116328 restraints weight = 5697.245| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.32 r_work: 0.3254 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6468 Z= 0.135 Angle : 0.547 11.573 8826 Z= 0.263 Chirality : 0.039 0.122 954 Planarity : 0.005 0.045 1095 Dihedral : 6.756 84.969 870 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.56 % Favored : 97.05 % Rotamer: Outliers : 2.50 % Allowed : 24.26 % Favored : 73.24 % 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: 3.22 (0.30), residues: 780 helix: 2.76 (0.21), residues: 573 sheet: None (None), residues: 0 loop : 0.34 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.011 0.001 TYR C 76 PHE 0.007 0.001 PHE C 195 TRP 0.009 0.001 TRP B 184 HIS 0.005 0.002 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 6465) covalent geometry : angle 0.54711 / 0.26 ( 8826) hydrogen bonds : bond 0.04226 / 2.92 ( 456) hydrogen bonds : angle 3.73910 / 2.72 ( 1341) Misc. bond : bond 0.00009 / 0.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.228 Fit side-chains REVERT: A 6 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7523 (pt0) REVERT: A 200 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7464 (t80) REVERT: A 203 LEU cc_start: 0.8377 (mt) cc_final: 0.8026 (tm) REVERT: B 200 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7414 (t80) REVERT: B 203 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7968 (tm) REVERT: C 200 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.7477 (t80) REVERT: C 203 LEU cc_start: 0.8389 (mt) cc_final: 0.8030 (tm) outliers start: 16 outliers final: 7 residues processed: 54 average time/residue: 0.3675 time to fit residues: 21.4779 Evaluate side-chains 58 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 200 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.142288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115924 restraints weight = 5781.569| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.34 r_work: 0.3251 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6468 Z= 0.134 Angle : 0.548 11.727 8826 Z= 0.262 Chirality : 0.039 0.123 954 Planarity : 0.005 0.044 1095 Dihedral : 6.742 84.773 870 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.44 % Favored : 97.18 % Rotamer: Outliers : 2.82 % Allowed : 23.94 % Favored : 73.24 % 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: 3.24 (0.30), residues: 780 helix: 2.78 (0.21), residues: 573 sheet: None (None), residues: 0 loop : 0.32 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.010 0.001 TYR C 86 PHE 0.007 0.001 PHE C 195 TRP 0.009 0.001 TRP B 184 HIS 0.005 0.002 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 6465) covalent geometry : angle 0.54756 / 0.26 ( 8826) hydrogen bonds : bond 0.04186 / 2.89 ( 456) hydrogen bonds : angle 3.73081 / 2.71 ( 1341) Misc. bond : bond 0.00008 / 0.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.155 Fit side-chains REVERT: A 6 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7514 (pt0) REVERT: A 200 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7460 (t80) REVERT: A 203 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8028 (tm) REVERT: B 200 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7419 (t80) REVERT: B 203 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7961 (tm) REVERT: C 200 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7484 (t80) REVERT: C 203 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8024 (tm) outliers start: 18 outliers final: 6 residues processed: 58 average time/residue: 0.3818 time to fit residues: 23.8242 Evaluate side-chains 57 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.142719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.116335 restraints weight = 5747.777| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.32 r_work: 0.3250 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6468 Z= 0.141 Angle : 0.559 12.091 8826 Z= 0.268 Chirality : 0.039 0.123 954 Planarity : 0.005 0.044 1095 Dihedral : 6.773 84.725 870 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.08 % Favored : 96.54 % Rotamer: Outliers : 2.50 % Allowed : 23.94 % Favored : 73.55 % 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: 3.23 (0.30), residues: 780 helix: 2.75 (0.21), residues: 573 sheet: None (None), residues: 0 loop : 0.40 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 243 TYR 0.010 0.001 TYR A 86 PHE 0.007 0.001 PHE A 195 TRP 0.009 0.001 TRP B 184 HIS 0.006 0.002 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 6465) covalent geometry : angle 0.55902 / 0.27 ( 8826) hydrogen bonds : bond 0.04234 / 2.91 ( 456) hydrogen bonds : angle 3.74621 / 2.72 ( 1341) Misc. bond : bond 0.00009 / 0.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.248 Fit side-chains REVERT: A 6 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7571 (pt0) REVERT: A 200 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7519 (t80) REVERT: A 203 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8095 (tm) REVERT: B 200 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7469 (t80) REVERT: B 203 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8021 (tm) REVERT: C 200 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7548 (t80) REVERT: C 203 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8089 (tm) outliers start: 16 outliers final: 7 residues processed: 52 average time/residue: 0.3933 time to fit residues: 22.1027 Evaluate side-chains 58 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.140970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114471 restraints weight = 5685.198| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.32 r_work: 0.3239 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6468 Z= 0.146 Angle : 0.565 12.471 8826 Z= 0.270 Chirality : 0.039 0.125 954 Planarity : 0.005 0.044 1095 Dihedral : 6.832 85.185 870 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.95 % Favored : 96.67 % Rotamer: Outliers : 2.50 % Allowed : 24.10 % Favored : 73.40 % 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: 3.21 (0.30), residues: 780 helix: 2.72 (0.21), residues: 573 sheet: None (None), residues: 0 loop : 0.45 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 191 TYR 0.011 0.001 TYR C 76 PHE 0.009 0.001 PHE A 195 TRP 0.009 0.001 TRP B 184 HIS 0.005 0.002 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 6465) covalent geometry : angle 0.56457 / 0.27 ( 8826) hydrogen bonds : bond 0.04289 / 2.95 ( 456) hydrogen bonds : angle 3.74733 / 2.72 ( 1341) Misc. bond : bond 0.00011 / 0.01 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.225 Fit side-chains REVERT: A 6 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7528 (pt0) REVERT: A 200 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7469 (t80) REVERT: A 203 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8050 (tm) REVERT: B 200 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7418 (t80) REVERT: B 203 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7973 (tm) REVERT: C 200 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7492 (t80) REVERT: C 203 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8044 (tm) outliers start: 16 outliers final: 6 residues processed: 51 average time/residue: 0.3719 time to fit residues: 20.4119 Evaluate side-chains 56 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.141553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.115002 restraints weight = 5780.070| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.34 r_work: 0.3191 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6468 Z= 0.135 Angle : 0.554 12.095 8826 Z= 0.266 Chirality : 0.039 0.123 954 Planarity : 0.005 0.044 1095 Dihedral : 6.790 84.737 870 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.82 % Favored : 96.79 % Rotamer: Outliers : 2.35 % Allowed : 24.41 % Favored : 73.24 % 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: 3.25 (0.30), residues: 780 helix: 2.74 (0.21), residues: 573 sheet: None (None), residues: 0 loop : 0.49 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 176 TYR 0.010 0.001 TYR A 86 PHE 0.007 0.001 PHE B 195 TRP 0.009 0.001 TRP A 184 HIS 0.005 0.002 HIS C 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 6465) covalent geometry : angle 0.55410 / 0.27 ( 8826) hydrogen bonds : bond 0.04213 / 2.90 ( 456) hydrogen bonds : angle 3.74813 / 2.72 ( 1341) Misc. bond : bond 0.00005 / 0.00 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2238.67 seconds wall clock time: 39 minutes 6.52 seconds (2346.52 seconds total)