Starting phenix.real_space_refine on Sat May 10 11:52:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxp_36708/05_2025/8jxp_36708_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxp_36708/05_2025/8jxp_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_36708/05_2025/8jxp_36708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxp_36708/05_2025/8jxp_36708.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxp_36708/05_2025/8jxp_36708_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxp_36708/05_2025/8jxp_36708_neut.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 26 Unusual residues: {' K': 6, 'RET': 1} Classifications: {'undetermined': 7} Link IDs: {None: 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: C, B Time building chain proxies: 8.43, per 1000 atoms: 1.34 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: 1.85 Conformation dependent library (CDL) restraints added in 857.1 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: 0.51 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: 1.71 Time building geometry restraints manager: 1.97 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 3.250 nonbonded pdb=" CG MET C 239 " pdb=" K K C 401 " model vdw 1.644 3.250 nonbonded pdb=" CG MET B 239 " pdb=" K K B 401 " model vdw 1.645 3.250 nonbonded pdb=" CB MET A 239 " pdb=" K K A 401 " model vdw 1.890 3.250 nonbonded pdb=" CB MET B 239 " pdb=" K K B 401 " model vdw 1.890 3.250 ... (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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 23.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.040 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.002 TRP A 219 HIS 0.005 0.002 HIS C 210 PHE 0.037 0.003 PHE A 143 TYR 0.010 0.002 TYR A 102 ARG 0.003 0.001 ARG B 176 Details of bonding type rmsd hydrogen bonds : bond 0.16354 ( 456) hydrogen bonds : angle 6.48951 ( 1341) covalent geometry : bond 0.00868 ( 6465) covalent geometry : angle 1.32543 ( 8826) Misc. bond : bond 0.05116 ( 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 : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7068 (mt) REVERT: A 203 LEU cc_start: 0.8053 (mt) cc_final: 0.7842 (tp) REVERT: B 126 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7089 (mt) REVERT: B 203 LEU cc_start: 0.8043 (mt) cc_final: 0.7810 (tp) REVERT: C 126 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7139 (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: 0.8651 time to fit residues: 209.5083 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 : 0.681 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.161903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.136294 restraints weight = 5954.860| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.47 r_work: 0.3810 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6468 Z= 0.160 Angle : 0.628 8.624 8826 Z= 0.324 Chirality : 0.040 0.130 954 Planarity : 0.007 0.081 1095 Dihedral : 10.503 68.811 929 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.77 % Allowed : 3.46 % Favored : 95.77 % Rotamer: Outliers : 7.51 % Allowed : 18.31 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.29), residues: 780 helix: 1.28 (0.20), residues: 573 sheet: None (None), residues: 0 loop : -0.58 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 198 HIS 0.004 0.002 HIS A 224 PHE 0.011 0.001 PHE A 195 TYR 0.017 0.002 TYR B 86 ARG 0.002 0.000 ARG C 243 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 456) hydrogen bonds : angle 4.06438 ( 1341) covalent geometry : bond 0.00360 ( 6465) covalent geometry : angle 0.62769 ( 8826) Misc. bond : bond 0.00095 ( 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 109 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 61 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7456 (pt0) REVERT: A 11 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.6850 (mp10) REVERT: A 13 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: A 203 LEU cc_start: 0.8157 (mt) cc_final: 0.7857 (tp) REVERT: B 6 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7559 (pt0) REVERT: B 13 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: B 203 LEU cc_start: 0.8118 (mt) cc_final: 0.7850 (tp) REVERT: C 6 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7552 (pt0) REVERT: C 13 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: C 203 LEU cc_start: 0.8189 (mt) cc_final: 0.7884 (tp) outliers start: 48 outliers final: 20 residues processed: 101 average time/residue: 0.7717 time to fit residues: 83.8443 Evaluate side-chains 67 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 43 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 64 LEU 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 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 35 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.128430 restraints weight = 6125.359| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.51 r_work: 0.3667 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4419 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= 0.143 Angle : 0.559 8.588 8826 Z= 0.284 Chirality : 0.039 0.115 954 Planarity : 0.006 0.060 1095 Dihedral : 9.177 80.747 900 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.77 % Allowed : 3.21 % Favored : 96.03 % Rotamer: Outliers : 4.38 % Allowed : 22.69 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.30), residues: 780 helix: 2.29 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 0.07 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 219 HIS 0.004 0.002 HIS A 224 PHE 0.009 0.001 PHE A 195 TYR 0.012 0.001 TYR B 86 ARG 0.005 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 456) hydrogen bonds : angle 3.86057 ( 1341) covalent geometry : bond 0.00321 ( 6465) covalent geometry : angle 0.55941 ( 8826) Misc. bond : bond 0.00093 ( 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 87 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 0.681 Fit side-chains REVERT: A 6 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7533 (pt0) REVERT: A 64 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7523 (tt) REVERT: A 200 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7396 (t80) REVERT: A 203 LEU cc_start: 0.8320 (mt) cc_final: 0.8019 (tp) REVERT: B 6 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7579 (pt0) REVERT: B 200 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7417 (t80) REVERT: B 203 LEU cc_start: 0.8326 (mt) cc_final: 0.7988 (tp) REVERT: C 6 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7628 (pt0) REVERT: C 200 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7461 (t80) REVERT: C 203 LEU cc_start: 0.8344 (mt) cc_final: 0.8012 (tp) outliers start: 28 outliers final: 8 residues processed: 81 average time/residue: 0.6900 time to fit residues: 61.0103 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 : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 64 LEU 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 Chi-restraints excluded: chain C residue 200 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.143631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.117655 restraints weight = 5879.825| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.27 r_work: 0.3281 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4706 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= 0.140 Angle : 0.554 10.702 8826 Z= 0.273 Chirality : 0.039 0.118 954 Planarity : 0.005 0.050 1095 Dihedral : 7.593 85.623 876 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.77 % Allowed : 2.69 % Favored : 96.54 % Rotamer: Outliers : 3.91 % Allowed : 22.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.30), residues: 780 helix: 2.43 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 0.39 (0.47), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 184 HIS 0.006 0.003 HIS B 210 PHE 0.008 0.001 PHE A 195 TYR 0.012 0.001 TYR C 86 ARG 0.001 0.000 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 456) hydrogen bonds : angle 3.79497 ( 1341) covalent geometry : bond 0.00320 ( 6465) covalent geometry : angle 0.55406 ( 8826) Misc. bond : bond 0.00015 ( 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 75 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 50 time to evaluate : 0.587 Fit side-chains REVERT: A 6 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7467 (pt0) REVERT: A 64 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7535 (tt) REVERT: A 200 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7456 (t80) REVERT: B 6 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7463 (pt0) REVERT: B 200 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7461 (t80) REVERT: C 6 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7570 (pt0) REVERT: C 200 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7519 (t80) outliers start: 25 outliers final: 13 residues processed: 69 average time/residue: 0.6687 time to fit residues: 50.5401 Evaluate side-chains 64 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 136 LEU 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 A residue 261 LEU Chi-restraints excluded: chain B residue 136 LEU 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 136 LEU Chi-restraints excluded: chain C residue 168 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 42 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.141012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115479 restraints weight = 5817.369| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.24 r_work: 0.3250 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4967 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= 0.148 Angle : 0.555 11.419 8826 Z= 0.271 Chirality : 0.039 0.119 954 Planarity : 0.005 0.047 1095 Dihedral : 7.722 87.754 876 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.46 % Favored : 96.15 % Rotamer: Outliers : 4.07 % Allowed : 23.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.30), residues: 780 helix: 2.51 (0.21), residues: 576 sheet: None (None), residues: 0 loop : 0.39 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 219 HIS 0.006 0.003 HIS B 210 PHE 0.008 0.001 PHE A 195 TYR 0.013 0.001 TYR C 76 ARG 0.002 0.000 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 456) hydrogen bonds : angle 3.79900 ( 1341) covalent geometry : bond 0.00344 ( 6465) covalent geometry : angle 0.55505 ( 8826) Misc. bond : bond 0.00014 ( 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: 26 poor density : 49 time to evaluate : 0.704 Fit side-chains REVERT: A 6 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7540 (pt0) REVERT: A 200 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7533 (t80) REVERT: A 203 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8102 (tm) REVERT: B 6 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7502 (pt0) REVERT: B 200 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7527 (t80) REVERT: B 203 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8076 (tm) REVERT: C 200 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7591 (t80) REVERT: C 203 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8097 (tm) outliers start: 26 outliers final: 13 residues processed: 60 average time/residue: 0.7339 time to fit residues: 48.1254 Evaluate side-chains 65 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 203 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 136 LEU 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 B residue 203 LEU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 168 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 43 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 66 optimal weight: 0.1980 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.140164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114544 restraints weight = 5805.093| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.30 r_work: 0.3184 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.5123 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= 0.147 Angle : 0.552 11.773 8826 Z= 0.268 Chirality : 0.039 0.122 954 Planarity : 0.005 0.045 1095 Dihedral : 7.674 86.514 876 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.21 % Favored : 96.41 % Rotamer: Outliers : 3.44 % Allowed : 23.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.30), residues: 780 helix: 2.59 (0.21), residues: 573 sheet: None (None), residues: 0 loop : 0.35 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 184 HIS 0.006 0.002 HIS B 210 PHE 0.008 0.001 PHE C 242 TYR 0.012 0.001 TYR C 76 ARG 0.002 0.000 ARG C 243 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 456) hydrogen bonds : angle 3.79090 ( 1341) covalent geometry : bond 0.00343 ( 6465) covalent geometry : angle 0.55249 ( 8826) Misc. bond : bond 0.00014 ( 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 81 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.690 Fit side-chains REVERT: A 200 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7489 (t80) REVERT: A 203 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8044 (tm) REVERT: B 200 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7470 (t80) REVERT: B 203 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8028 (tm) REVERT: C 200 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7553 (t80) REVERT: C 203 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8035 (tm) outliers start: 22 outliers final: 11 residues processed: 67 average time/residue: 0.6686 time to fit residues: 49.1916 Evaluate side-chains 69 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 121 ASN 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 A residue 203 LEU 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 168 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 168 LEU Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3630 r_free = 0.3630 target = 0.138083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112172 restraints weight = 5786.334| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.30 r_work: 0.3168 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6468 Z= 0.161 Angle : 0.573 12.463 8826 Z= 0.278 Chirality : 0.040 0.125 954 Planarity : 0.005 0.044 1095 Dihedral : 7.726 86.127 876 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.33 % Favored : 96.28 % Rotamer: Outliers : 3.60 % Allowed : 23.79 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.30), residues: 780 helix: 2.59 (0.21), residues: 573 sheet: None (None), residues: 0 loop : 0.37 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 184 HIS 0.007 0.003 HIS B 210 PHE 0.009 0.001 PHE C 251 TYR 0.012 0.001 TYR C 76 ARG 0.002 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 456) hydrogen bonds : angle 3.79145 ( 1341) covalent geometry : bond 0.00380 ( 6465) covalent geometry : angle 0.57340 ( 8826) Misc. bond : bond 0.00018 ( 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 69 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.689 Fit side-chains REVERT: A 200 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7497 (t80) REVERT: A 203 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8087 (tm) REVERT: B 200 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7484 (t80) REVERT: B 203 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8057 (tm) REVERT: C 200 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7545 (t80) REVERT: C 203 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8083 (tm) outliers start: 23 outliers final: 10 residues processed: 54 average time/residue: 0.7883 time to fit residues: 46.4394 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 : 0.697 ------------------------------------------------------------------------------- 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 168 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 136 LEU 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 B residue 203 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 203 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 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 = 0.3659 r_free = 0.3659 target = 0.140133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114326 restraints weight = 5798.118| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.31 r_work: 0.3184 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.5272 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 : 0.550 11.873 8826 Z= 0.266 Chirality : 0.039 0.122 954 Planarity : 0.005 0.044 1095 Dihedral : 7.616 85.195 876 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.33 % Favored : 96.28 % Rotamer: Outliers : 2.66 % Allowed : 24.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.30), residues: 780 helix: 2.64 (0.21), residues: 573 sheet: None (None), residues: 0 loop : 0.45 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 184 HIS 0.006 0.002 HIS B 210 PHE 0.007 0.001 PHE A 242 TYR 0.011 0.001 TYR C 76 ARG 0.001 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 456) hydrogen bonds : angle 3.77971 ( 1341) covalent geometry : bond 0.00325 ( 6465) covalent geometry : angle 0.54954 ( 8826) Misc. bond : bond 0.00011 ( 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 67 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.717 Fit side-chains REVERT: A 200 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7468 (t80) REVERT: A 203 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8027 (tm) REVERT: B 200 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7457 (t80) REVERT: B 203 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8034 (tm) REVERT: C 200 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7519 (t80) REVERT: C 203 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8058 (tm) outliers start: 17 outliers final: 10 residues processed: 56 average time/residue: 0.7865 time to fit residues: 48.0573 Evaluate side-chains 65 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 168 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 136 LEU 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 B residue 203 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 168 LEU 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: 0.7980 chunk 77 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 0.0060 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 62 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.142568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.117429 restraints weight = 5841.103| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.25 r_work: 0.3239 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.5357 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= 0.119 Angle : 0.521 10.825 8826 Z= 0.254 Chirality : 0.038 0.117 954 Planarity : 0.005 0.044 1095 Dihedral : 7.398 83.510 876 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.95 % Favored : 96.67 % Rotamer: Outliers : 2.35 % Allowed : 24.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.30), residues: 780 helix: 2.76 (0.21), residues: 573 sheet: None (None), residues: 0 loop : 0.52 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 184 HIS 0.004 0.002 HIS B 210 PHE 0.007 0.001 PHE A 242 TYR 0.010 0.001 TYR C 86 ARG 0.001 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 456) hydrogen bonds : angle 3.74586 ( 1341) covalent geometry : bond 0.00262 ( 6465) covalent geometry : angle 0.52135 ( 8826) Misc. bond : bond 0.00003 ( 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 65 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.728 Fit side-chains REVERT: A 200 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7559 (t80) REVERT: A 203 LEU cc_start: 0.8475 (mt) cc_final: 0.8142 (tm) REVERT: B 200 PHE cc_start: 0.7856 (OUTLIER) cc_final: 0.7552 (t80) REVERT: B 203 LEU cc_start: 0.8436 (mt) cc_final: 0.8120 (tm) REVERT: C 200 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7609 (t80) REVERT: C 203 LEU cc_start: 0.8474 (mt) cc_final: 0.8149 (tm) outliers start: 15 outliers final: 7 residues processed: 56 average time/residue: 0.8127 time to fit residues: 49.4197 Evaluate side-chains 55 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN 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 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 C residue 136 LEU Chi-restraints excluded: chain C residue 200 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 0.0670 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.141429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116070 restraints weight = 5842.318| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.24 r_work: 0.3195 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.5386 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= 0.129 Angle : 0.537 11.497 8826 Z= 0.261 Chirality : 0.038 0.119 954 Planarity : 0.005 0.043 1095 Dihedral : 7.012 84.353 872 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.95 % Favored : 96.67 % Rotamer: Outliers : 2.03 % Allowed : 24.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.30), residues: 780 helix: 2.75 (0.21), residues: 573 sheet: None (None), residues: 0 loop : 0.57 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 184 HIS 0.005 0.002 HIS B 210 PHE 0.007 0.001 PHE A 242 TYR 0.010 0.001 TYR B 86 ARG 0.001 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 456) hydrogen bonds : angle 3.74201 ( 1341) covalent geometry : bond 0.00294 ( 6465) covalent geometry : angle 0.53727 ( 8826) Misc. bond : bond 0.00008 ( 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: 13 poor density : 47 time to evaluate : 0.690 Fit side-chains REVERT: A 200 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7589 (t80) REVERT: A 203 LEU cc_start: 0.8488 (mt) cc_final: 0.8165 (tm) REVERT: B 200 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7585 (t80) REVERT: B 203 LEU cc_start: 0.8458 (mt) cc_final: 0.8152 (tm) REVERT: C 200 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7640 (t80) REVERT: C 203 LEU cc_start: 0.8488 (mt) cc_final: 0.8174 (tm) outliers start: 13 outliers final: 8 residues processed: 52 average time/residue: 0.8346 time to fit residues: 47.0727 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 : 0.710 ------------------------------------------------------------------------------- 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 168 LEU 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 C residue 136 LEU Chi-restraints excluded: chain C residue 200 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.138721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113247 restraints weight = 5927.536| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.26 r_work: 0.3141 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6468 Z= 0.158 Angle : 0.573 12.811 8826 Z= 0.277 Chirality : 0.040 0.127 954 Planarity : 0.005 0.043 1095 Dihedral : 7.210 85.653 872 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.29), residues: 780 helix: 2.63 (0.21), residues: 573 sheet: None (None), residues: 0 loop : 0.60 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 184 HIS 0.006 0.002 HIS B 210 PHE 0.007 0.001 PHE A 242 TYR 0.011 0.001 TYR B 76 ARG 0.002 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 456) hydrogen bonds : angle 3.78140 ( 1341) covalent geometry : bond 0.00372 ( 6465) covalent geometry : angle 0.57342 ( 8826) Misc. bond : bond 0.00017 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4632.88 seconds wall clock time: 81 minutes 46.48 seconds (4906.48 seconds total)