Starting phenix.real_space_refine on Tue Feb 3 21:59:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e04_47348/02_2026/9e04_47348.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e04_47348/02_2026/9e04_47348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e04_47348/02_2026/9e04_47348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e04_47348/02_2026/9e04_47348.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e04_47348/02_2026/9e04_47348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e04_47348/02_2026/9e04_47348.map" } resolution = 3.2 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= 0.001 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 4935 2.51 5 N 1101 2.21 5 O 1167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7239 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 148 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "B" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 370 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "A" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1895 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 11, 'TRANS': 227} Chain breaks: 1 Chain: "D" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 370 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "F" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 370 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "E" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1895 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 11, 'TRANS': 227} Chain breaks: 1 Chain: "C" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1895 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 11, 'TRANS': 227} Chain breaks: 1 Chain: "I" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 148 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "G" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 148 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Time building chain proxies: 1.21, per 1000 atoms: 0.17 Number of scatterers: 7239 At special positions: 0 Unit cell: (94.848, 98.176, 89.024, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1167 8.00 N 1101 7.00 C 4935 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=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 211.5 milliseconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 2 sheets defined 87.9% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'H' and resid 2 through 17 Processing helix chain 'B' and resid 5 through 20 Processing helix chain 'B' and resid 25 through 47 Processing helix chain 'A' and resid 5 through 33 removed outlier: 4.350A pdb=" N GLU A 11 " --> pdb=" O PRO A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 61 Proline residue: A 44 - end of helix Processing helix chain 'A' and resid 165 through 196 Proline residue: A 185 - end of helix Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 203 through 228 Proline residue: A 209 - end of helix Processing helix chain 'A' and resid 229 through 241 removed outlier: 3.574A pdb=" N GLN A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 281 removed outlier: 3.819A pdb=" N GLY A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) Proline residue: A 272 - end of helix removed outlier: 3.925A pdb=" N TYR A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.804A pdb=" N TYR A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 308 removed outlier: 3.898A pdb=" N VAL A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 335 Proline residue: A 321 - end of helix Processing helix chain 'D' and resid 5 through 20 Processing helix chain 'D' and resid 24 through 47 Processing helix chain 'F' and resid 5 through 20 Processing helix chain 'F' and resid 24 through 47 Processing helix chain 'E' and resid 5 through 33 removed outlier: 4.347A pdb=" N GLU E 11 " --> pdb=" O PRO E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 61 Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 165 through 196 Proline residue: E 185 - end of helix Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 203 through 228 Proline residue: E 209 - end of helix Processing helix chain 'E' and resid 229 through 241 removed outlier: 3.509A pdb=" N GLN E 235 " --> pdb=" O PRO E 231 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 281 removed outlier: 3.858A pdb=" N GLY E 256 " --> pdb=" O GLU E 252 " (cutoff:3.500A) Proline residue: E 272 - end of helix removed outlier: 3.938A pdb=" N TYR E 276 " --> pdb=" O PRO E 272 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU E 281 " --> pdb=" O PHE E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 292 removed outlier: 3.863A pdb=" N TYR E 292 " --> pdb=" O THR E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 308 removed outlier: 3.901A pdb=" N VAL E 298 " --> pdb=" O LYS E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 336 Proline residue: E 321 - end of helix Processing helix chain 'C' and resid 5 through 33 removed outlier: 4.488A pdb=" N GLU C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 61 Proline residue: C 44 - end of helix Processing helix chain 'C' and resid 165 through 196 Proline residue: C 185 - end of helix Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 203 through 228 Proline residue: C 209 - end of helix Processing helix chain 'C' and resid 229 through 241 removed outlier: 3.592A pdb=" N GLN C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 281 removed outlier: 3.898A pdb=" N GLY C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) Proline residue: C 272 - end of helix removed outlier: 3.943A pdb=" N TYR C 276 " --> pdb=" O PRO C 272 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU C 281 " --> pdb=" O PHE C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.790A pdb=" N TYR C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 308 removed outlier: 3.829A pdb=" N VAL C 298 " --> pdb=" O LYS C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 335 Proline residue: C 321 - end of helix Processing helix chain 'I' and resid 2 through 17 Processing helix chain 'G' and resid 2 through 17 Processing sheet with id=AA1, first strand: chain 'A' and resid 249 through 250 removed outlier: 6.194A pdb=" N THR E 246 " --> pdb=" O THR C 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 247 removed outlier: 6.147A pdb=" N THR A 246 " --> pdb=" O THR E 161 " (cutoff:3.500A) 593 hydrogen bonds defined for protein. 1773 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: 0.91 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2084 1.35 - 1.46: 1874 1.46 - 1.58: 3392 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 7422 Sorted by residual: bond pdb=" C LEU B 25 " pdb=" N PRO B 26 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.13e+00 bond pdb=" C LEU F 25 " pdb=" N PRO F 26 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.75e+00 bond pdb=" C LEU D 25 " pdb=" N PRO D 26 " ideal model delta sigma weight residual 1.335 1.358 -0.022 1.36e-02 5.41e+03 2.71e+00 bond pdb=" C LYS E 6 " pdb=" N PRO E 7 " ideal model delta sigma weight residual 1.337 1.354 -0.018 1.11e-02 8.12e+03 2.62e+00 bond pdb=" C LYS A 6 " pdb=" N PRO A 7 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.19e-02 7.06e+03 2.28e+00 ... (remaining 7417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 9809 1.68 - 3.37: 206 3.37 - 5.05: 37 5.05 - 6.73: 7 6.73 - 8.42: 6 Bond angle restraints: 10065 Sorted by residual: angle pdb=" CB MET C 206 " pdb=" CG MET C 206 " pdb=" SD MET C 206 " ideal model delta sigma weight residual 112.70 121.12 -8.42 3.00e+00 1.11e-01 7.87e+00 angle pdb=" N GLU A 270 " pdb=" CA GLU A 270 " pdb=" C GLU A 270 " ideal model delta sigma weight residual 111.36 114.42 -3.06 1.09e+00 8.42e-01 7.87e+00 angle pdb=" CB MET E 206 " pdb=" CG MET E 206 " pdb=" SD MET E 206 " ideal model delta sigma weight residual 112.70 121.10 -8.40 3.00e+00 1.11e-01 7.85e+00 angle pdb=" N GLU E 270 " pdb=" CA GLU E 270 " pdb=" C GLU E 270 " ideal model delta sigma weight residual 111.36 114.36 -3.00 1.09e+00 8.42e-01 7.56e+00 angle pdb=" C ALA C 196 " pdb=" N PRO C 197 " pdb=" CA PRO C 197 " ideal model delta sigma weight residual 119.84 116.42 3.42 1.25e+00 6.40e-01 7.49e+00 ... (remaining 10060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 3638 17.17 - 34.34: 472 34.34 - 51.52: 147 51.52 - 68.69: 35 68.69 - 85.86: 4 Dihedral angle restraints: 4296 sinusoidal: 1653 harmonic: 2643 Sorted by residual: dihedral pdb=" CA LYS B 24 " pdb=" C LYS B 24 " pdb=" N LEU B 25 " pdb=" CA LEU B 25 " ideal model delta harmonic sigma weight residual 180.00 161.66 18.34 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CB GLU F 45 " pdb=" CG GLU F 45 " pdb=" CD GLU F 45 " pdb=" OE1 GLU F 45 " ideal model delta sinusoidal sigma weight residual 0.00 85.86 -85.86 1 3.00e+01 1.11e-03 9.90e+00 dihedral pdb=" CG LYS A 54 " pdb=" CD LYS A 54 " pdb=" CE LYS A 54 " pdb=" NZ LYS A 54 " ideal model delta sinusoidal sigma weight residual 60.00 119.71 -59.71 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 793 0.037 - 0.073: 324 0.073 - 0.110: 75 0.110 - 0.147: 10 0.147 - 0.183: 1 Chirality restraints: 1203 Sorted by residual: chirality pdb=" CB THR C 259 " pdb=" CA THR C 259 " pdb=" OG1 THR C 259 " pdb=" CG2 THR C 259 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CB VAL E 333 " pdb=" CA VAL E 333 " pdb=" CG1 VAL E 333 " pdb=" CG2 VAL E 333 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE F 9 " pdb=" N ILE F 9 " pdb=" C ILE F 9 " pdb=" CB ILE F 9 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 ... (remaining 1200 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 271 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO A 272 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 271 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO C 272 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 272 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 272 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 271 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO E 272 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO E 272 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 272 " -0.022 5.00e-02 4.00e+02 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 244 2.72 - 3.26: 7373 3.26 - 3.81: 12256 3.81 - 4.35: 13872 4.35 - 4.90: 24399 Nonbonded interactions: 58144 Sorted by model distance: nonbonded pdb=" OG1 THR A 285 " pdb=" OD1 ASP A 286 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR C 285 " pdb=" OD1 ASP C 286 " model vdw 2.269 3.040 nonbonded pdb=" O GLN C 235 " pdb=" OG1 THR C 239 " model vdw 2.284 3.040 nonbonded pdb=" O PHE A 194 " pdb=" NH1 ARG G 3 " model vdw 2.286 3.120 nonbonded pdb=" OG1 THR E 285 " pdb=" OD1 ASP E 286 " model vdw 2.296 3.040 ... (remaining 58139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.050 Find NCS groups from input model: 0.070 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.004 0.033 7422 Z= 0.172 Angle : 0.644 8.417 10065 Z= 0.363 Chirality : 0.040 0.183 1203 Planarity : 0.004 0.048 1206 Dihedral : 17.236 85.860 2592 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.73 % Allowed : 30.73 % Favored : 66.54 % 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: 2.28 (0.29), residues: 894 helix: 2.39 (0.18), residues: 753 sheet: None (None), residues: 0 loop : -3.78 (0.45), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 3 TYR 0.010 0.001 TYR C 200 PHE 0.018 0.001 PHE C 257 TRP 0.006 0.001 TRP C 40 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7422) covalent geometry : angle 0.64365 (10065) hydrogen bonds : bond 0.11937 ( 593) hydrogen bonds : angle 4.74068 ( 1773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.268 Fit side-chains REVERT: A 16 LEU cc_start: 0.8165 (mt) cc_final: 0.7946 (mp) REVERT: A 206 MET cc_start: 0.7780 (mmp) cc_final: 0.7416 (mmp) REVERT: A 328 LEU cc_start: 0.8217 (tp) cc_final: 0.8011 (tt) REVERT: E 61 MET cc_start: 0.4516 (tmm) cc_final: 0.4237 (tmm) REVERT: E 191 LEU cc_start: 0.8533 (tt) cc_final: 0.8312 (tt) REVERT: E 219 LEU cc_start: 0.8102 (tp) cc_final: 0.7868 (tt) REVERT: E 293 PHE cc_start: 0.7044 (t80) cc_final: 0.6676 (t80) REVERT: C 158 MET cc_start: 0.6454 (tpp) cc_final: 0.5540 (pmm) REVERT: C 161 THR cc_start: 0.8417 (m) cc_final: 0.8175 (t) REVERT: C 208 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7344 (mt) REVERT: C 293 PHE cc_start: 0.6871 (t80) cc_final: 0.6453 (t80) outliers start: 21 outliers final: 19 residues processed: 151 average time/residue: 0.0493 time to fit residues: 11.4994 Evaluate side-chains 153 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 ASP Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.0870 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.128732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115829 restraints weight = 9601.561| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.23 r_work: 0.3287 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7422 Z= 0.134 Angle : 0.520 6.315 10065 Z= 0.258 Chirality : 0.040 0.127 1203 Planarity : 0.004 0.036 1206 Dihedral : 6.511 57.829 997 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.43 % Allowed : 26.82 % Favored : 68.75 % 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: 2.68 (0.29), residues: 894 helix: 2.60 (0.18), residues: 762 sheet: None (None), residues: 0 loop : -3.61 (0.47), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 15 TYR 0.008 0.001 TYR C 200 PHE 0.016 0.001 PHE A 293 TRP 0.010 0.001 TRP C 192 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7422) covalent geometry : angle 0.51959 (10065) hydrogen bonds : bond 0.03767 ( 593) hydrogen bonds : angle 3.80801 ( 1773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.208 Fit side-chains REVERT: B 45 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6484 (tm-30) REVERT: A 206 MET cc_start: 0.7750 (mmp) cc_final: 0.7350 (mmp) REVERT: A 328 LEU cc_start: 0.8235 (tp) cc_final: 0.7986 (tt) REVERT: E 61 MET cc_start: 0.4571 (tmm) cc_final: 0.4319 (tmm) REVERT: E 205 LYS cc_start: 0.7314 (ptpp) cc_final: 0.6970 (ptpp) REVERT: E 219 LEU cc_start: 0.8136 (tp) cc_final: 0.7909 (tt) REVERT: E 299 ILE cc_start: 0.8160 (mt) cc_final: 0.7959 (mm) REVERT: C 158 MET cc_start: 0.6415 (tpp) cc_final: 0.5630 (pmm) REVERT: C 161 THR cc_start: 0.8401 (m) cc_final: 0.8159 (t) REVERT: C 208 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7454 (mt) REVERT: G 13 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7720 (mp) outliers start: 34 outliers final: 21 residues processed: 168 average time/residue: 0.0501 time to fit residues: 12.7984 Evaluate side-chains 163 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain G residue 13 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 77 optimal weight: 0.2980 chunk 75 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.127738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115006 restraints weight = 9513.670| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.22 r_work: 0.3272 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7422 Z= 0.153 Angle : 0.531 6.072 10065 Z= 0.264 Chirality : 0.041 0.164 1203 Planarity : 0.004 0.033 1206 Dihedral : 6.107 56.348 984 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.08 % Allowed : 26.04 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.28), residues: 894 helix: 2.52 (0.18), residues: 762 sheet: None (None), residues: 0 loop : -3.50 (0.47), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 15 TYR 0.010 0.001 TYR C 200 PHE 0.023 0.001 PHE C 27 TRP 0.009 0.001 TRP C 192 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7422) covalent geometry : angle 0.53078 (10065) hydrogen bonds : bond 0.03810 ( 593) hydrogen bonds : angle 3.80535 ( 1773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.271 Fit side-chains REVERT: B 45 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6509 (tm-30) REVERT: A 206 MET cc_start: 0.7735 (mmp) cc_final: 0.7341 (mmp) REVERT: E 61 MET cc_start: 0.4604 (tmm) cc_final: 0.4368 (tmm) REVERT: E 205 LYS cc_start: 0.7345 (ptpp) cc_final: 0.6997 (ptpp) REVERT: E 219 LEU cc_start: 0.8170 (tp) cc_final: 0.7933 (tt) REVERT: E 333 VAL cc_start: 0.7540 (m) cc_final: 0.7325 (t) REVERT: C 12 LEU cc_start: 0.8227 (tp) cc_final: 0.8012 (tp) REVERT: C 158 MET cc_start: 0.6377 (tpp) cc_final: 0.5598 (pmm) REVERT: C 161 THR cc_start: 0.8392 (m) cc_final: 0.8124 (t) REVERT: G 13 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7806 (mp) outliers start: 39 outliers final: 27 residues processed: 176 average time/residue: 0.0578 time to fit residues: 15.6233 Evaluate side-chains 175 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain G residue 13 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.126385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113540 restraints weight = 9605.253| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.24 r_work: 0.3248 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7422 Z= 0.173 Angle : 0.540 5.769 10065 Z= 0.270 Chirality : 0.042 0.152 1203 Planarity : 0.004 0.035 1206 Dihedral : 6.048 55.494 984 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.56 % Allowed : 26.30 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.28), residues: 894 helix: 2.36 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -3.40 (0.46), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 15 TYR 0.011 0.001 TYR C 200 PHE 0.015 0.001 PHE E 258 TRP 0.010 0.002 TRP C 192 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 7422) covalent geometry : angle 0.54034 (10065) hydrogen bonds : bond 0.03897 ( 593) hydrogen bonds : angle 3.83663 ( 1773) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.279 Fit side-chains REVERT: B 45 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6561 (tm-30) REVERT: A 206 MET cc_start: 0.7818 (mmp) cc_final: 0.7463 (mmp) REVERT: D 45 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6235 (tm-30) REVERT: E 20 VAL cc_start: 0.8044 (t) cc_final: 0.7831 (t) REVERT: E 61 MET cc_start: 0.4681 (tmm) cc_final: 0.4425 (tmm) REVERT: E 205 LYS cc_start: 0.7343 (ptpp) cc_final: 0.6978 (ptpp) REVERT: E 219 LEU cc_start: 0.8171 (tp) cc_final: 0.7937 (tt) REVERT: E 333 VAL cc_start: 0.7564 (m) cc_final: 0.7350 (t) REVERT: C 158 MET cc_start: 0.6361 (tpp) cc_final: 0.5584 (pmm) REVERT: C 161 THR cc_start: 0.8402 (m) cc_final: 0.8141 (t) REVERT: G 13 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7766 (mp) outliers start: 35 outliers final: 26 residues processed: 175 average time/residue: 0.0582 time to fit residues: 15.5047 Evaluate side-chains 179 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain G residue 13 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.127069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114333 restraints weight = 9632.745| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.25 r_work: 0.3247 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7422 Z= 0.165 Angle : 0.538 6.122 10065 Z= 0.267 Chirality : 0.041 0.157 1203 Planarity : 0.004 0.035 1206 Dihedral : 5.967 59.564 984 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.21 % Allowed : 26.95 % Favored : 67.84 % 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: 2.38 (0.28), residues: 894 helix: 2.34 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -3.25 (0.47), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 15 TYR 0.009 0.001 TYR C 200 PHE 0.017 0.001 PHE B 19 TRP 0.009 0.002 TRP C 192 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7422) covalent geometry : angle 0.53759 (10065) hydrogen bonds : bond 0.03788 ( 593) hydrogen bonds : angle 3.81692 ( 1773) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.276 Fit side-chains REVERT: B 45 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6587 (tm-30) REVERT: A 206 MET cc_start: 0.7797 (mmp) cc_final: 0.7447 (mmp) REVERT: D 45 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6246 (tm-30) REVERT: E 20 VAL cc_start: 0.8037 (t) cc_final: 0.7825 (t) REVERT: E 219 LEU cc_start: 0.8161 (tp) cc_final: 0.7930 (tt) REVERT: C 158 MET cc_start: 0.6369 (tpp) cc_final: 0.5563 (pmm) REVERT: C 161 THR cc_start: 0.8398 (m) cc_final: 0.8141 (t) REVERT: C 208 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7561 (mt) REVERT: C 262 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8119 (mt) REVERT: G 13 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7833 (mp) outliers start: 40 outliers final: 28 residues processed: 180 average time/residue: 0.0555 time to fit residues: 15.1463 Evaluate side-chains 183 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain G residue 13 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 0.0980 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.125451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112153 restraints weight = 9638.229| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.33 r_work: 0.3223 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7422 Z= 0.165 Angle : 0.542 8.154 10065 Z= 0.268 Chirality : 0.042 0.192 1203 Planarity : 0.004 0.036 1206 Dihedral : 5.816 56.662 984 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.21 % Allowed : 26.56 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.28), residues: 894 helix: 2.33 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -3.18 (0.47), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 15 TYR 0.009 0.001 TYR C 200 PHE 0.018 0.001 PHE B 19 TRP 0.009 0.002 TRP C 192 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7422) covalent geometry : angle 0.54193 (10065) hydrogen bonds : bond 0.03783 ( 593) hydrogen bonds : angle 3.80512 ( 1773) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.317 Fit side-chains REVERT: B 45 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6586 (tm-30) REVERT: A 206 MET cc_start: 0.7832 (mmp) cc_final: 0.7417 (mmp) REVERT: A 208 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7338 (mt) REVERT: D 45 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6333 (tm-30) REVERT: E 20 VAL cc_start: 0.7864 (t) cc_final: 0.7658 (t) REVERT: E 219 LEU cc_start: 0.8073 (tp) cc_final: 0.7842 (tt) REVERT: C 158 MET cc_start: 0.6234 (tpp) cc_final: 0.5151 (pmm) REVERT: C 161 THR cc_start: 0.8398 (m) cc_final: 0.8080 (t) REVERT: C 208 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7397 (mt) REVERT: G 13 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7722 (mp) outliers start: 40 outliers final: 29 residues processed: 178 average time/residue: 0.0583 time to fit residues: 15.8128 Evaluate side-chains 184 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain G residue 13 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.126070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.112526 restraints weight = 9603.520| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.40 r_work: 0.3213 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7422 Z= 0.169 Angle : 0.550 8.005 10065 Z= 0.270 Chirality : 0.041 0.168 1203 Planarity : 0.004 0.036 1206 Dihedral : 5.646 53.222 984 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.69 % Allowed : 26.30 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.28), residues: 894 helix: 2.31 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -3.07 (0.47), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 15 TYR 0.010 0.001 TYR C 200 PHE 0.019 0.001 PHE B 19 TRP 0.011 0.002 TRP C 192 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 7422) covalent geometry : angle 0.55002 (10065) hydrogen bonds : bond 0.03800 ( 593) hydrogen bonds : angle 3.82281 ( 1773) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.274 Fit side-chains REVERT: B 45 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: A 206 MET cc_start: 0.7914 (mmp) cc_final: 0.7505 (mmp) REVERT: D 45 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6371 (tm-30) REVERT: E 20 VAL cc_start: 0.8001 (t) cc_final: 0.7794 (t) REVERT: E 27 PHE cc_start: 0.8337 (t80) cc_final: 0.8077 (t80) REVERT: E 219 LEU cc_start: 0.8147 (tp) cc_final: 0.7921 (tt) REVERT: E 299 ILE cc_start: 0.8282 (mm) cc_final: 0.8047 (mt) REVERT: C 158 MET cc_start: 0.6316 (tpp) cc_final: 0.5373 (pmm) REVERT: C 161 THR cc_start: 0.8427 (m) cc_final: 0.8140 (t) REVERT: C 208 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7524 (mt) REVERT: G 13 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7838 (mp) outliers start: 36 outliers final: 29 residues processed: 174 average time/residue: 0.0583 time to fit residues: 15.3421 Evaluate side-chains 183 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain G residue 13 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.125619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.112406 restraints weight = 9617.373| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.33 r_work: 0.3228 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7422 Z= 0.162 Angle : 0.541 6.134 10065 Z= 0.267 Chirality : 0.041 0.172 1203 Planarity : 0.004 0.036 1206 Dihedral : 5.522 53.928 981 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.08 % Allowed : 25.78 % Favored : 69.14 % 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: 2.43 (0.28), residues: 894 helix: 2.33 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -2.88 (0.49), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 15 TYR 0.009 0.001 TYR C 200 PHE 0.017 0.001 PHE B 19 TRP 0.011 0.002 TRP C 192 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 7422) covalent geometry : angle 0.54095 (10065) hydrogen bonds : bond 0.03721 ( 593) hydrogen bonds : angle 3.79254 ( 1773) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.282 Fit side-chains REVERT: A 206 MET cc_start: 0.7851 (mmp) cc_final: 0.7430 (mmp) REVERT: D 45 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6350 (tm-30) REVERT: F 1 MET cc_start: -0.3289 (mmm) cc_final: -0.3933 (mmm) REVERT: E 20 VAL cc_start: 0.7950 (t) cc_final: 0.7744 (t) REVERT: E 27 PHE cc_start: 0.8319 (t80) cc_final: 0.8053 (t80) REVERT: E 219 LEU cc_start: 0.8114 (tp) cc_final: 0.7886 (tt) REVERT: C 158 MET cc_start: 0.6272 (tpp) cc_final: 0.5285 (pmm) REVERT: C 161 THR cc_start: 0.8409 (m) cc_final: 0.8118 (t) REVERT: C 208 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7498 (mt) REVERT: G 13 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7814 (mp) outliers start: 39 outliers final: 29 residues processed: 175 average time/residue: 0.0562 time to fit residues: 15.0237 Evaluate side-chains 181 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain G residue 13 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 70 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.127343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114388 restraints weight = 9490.336| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.25 r_work: 0.3251 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7422 Z= 0.148 Angle : 0.545 5.971 10065 Z= 0.266 Chirality : 0.041 0.170 1203 Planarity : 0.004 0.036 1206 Dihedral : 5.450 53.598 981 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.43 % Allowed : 26.17 % Favored : 69.40 % 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: 2.56 (0.28), residues: 894 helix: 2.40 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -2.72 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 15 TYR 0.009 0.001 TYR C 200 PHE 0.016 0.001 PHE B 19 TRP 0.011 0.001 TRP C 192 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7422) covalent geometry : angle 0.54534 (10065) hydrogen bonds : bond 0.03615 ( 593) hydrogen bonds : angle 3.75617 ( 1773) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.272 Fit side-chains REVERT: A 206 MET cc_start: 0.7779 (mmp) cc_final: 0.7341 (mmp) REVERT: D 45 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6334 (tm-30) REVERT: F 1 MET cc_start: -0.3325 (mmm) cc_final: -0.4031 (mmm) REVERT: E 27 PHE cc_start: 0.8305 (t80) cc_final: 0.8027 (t80) REVERT: E 219 LEU cc_start: 0.8092 (tp) cc_final: 0.7867 (tt) REVERT: E 299 ILE cc_start: 0.8151 (mm) cc_final: 0.7901 (mt) REVERT: C 158 MET cc_start: 0.6226 (tpp) cc_final: 0.5219 (pmm) REVERT: C 161 THR cc_start: 0.8389 (m) cc_final: 0.8086 (t) REVERT: G 13 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7775 (mp) outliers start: 34 outliers final: 27 residues processed: 169 average time/residue: 0.0565 time to fit residues: 14.1849 Evaluate side-chains 176 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain G residue 13 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 63 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 42 optimal weight: 0.0170 chunk 74 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.127253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.113972 restraints weight = 9621.952| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.32 r_work: 0.3238 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7422 Z= 0.150 Angle : 0.554 6.240 10065 Z= 0.270 Chirality : 0.041 0.179 1203 Planarity : 0.004 0.036 1206 Dihedral : 5.308 53.384 977 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.78 % Allowed : 26.56 % Favored : 69.66 % 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: 2.56 (0.28), residues: 894 helix: 2.39 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -2.64 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 15 TYR 0.009 0.001 TYR C 200 PHE 0.017 0.001 PHE B 19 TRP 0.011 0.001 TRP C 192 HIS 0.003 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7422) covalent geometry : angle 0.55403 (10065) hydrogen bonds : bond 0.03631 ( 593) hydrogen bonds : angle 3.76465 ( 1773) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.282 Fit side-chains REVERT: A 206 MET cc_start: 0.7790 (mmp) cc_final: 0.7357 (mmp) REVERT: D 45 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6368 (tm-30) REVERT: F 1 MET cc_start: -0.3267 (mmm) cc_final: -0.4133 (mmm) REVERT: E 27 PHE cc_start: 0.8306 (t80) cc_final: 0.8024 (t80) REVERT: E 219 LEU cc_start: 0.8098 (tp) cc_final: 0.7873 (tt) REVERT: C 158 MET cc_start: 0.6248 (tpp) cc_final: 0.5231 (pmm) REVERT: C 161 THR cc_start: 0.8398 (m) cc_final: 0.8092 (t) REVERT: G 13 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7790 (mp) outliers start: 29 outliers final: 24 residues processed: 165 average time/residue: 0.0552 time to fit residues: 13.6617 Evaluate side-chains 173 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 206 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain G residue 13 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.0170 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 20 optimal weight: 0.0980 chunk 41 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.128315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.114966 restraints weight = 9680.661| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.33 r_work: 0.3252 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7422 Z= 0.125 Angle : 0.530 6.438 10065 Z= 0.258 Chirality : 0.040 0.166 1203 Planarity : 0.004 0.036 1206 Dihedral : 5.135 53.012 975 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.26 % Allowed : 26.95 % Favored : 69.79 % 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: 2.86 (0.28), residues: 894 helix: 2.59 (0.18), residues: 759 sheet: None (None), residues: 0 loop : -2.56 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 15 TYR 0.007 0.001 TYR C 200 PHE 0.016 0.001 PHE B 19 TRP 0.010 0.001 TRP C 192 HIS 0.002 0.001 HIS A 34 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7422) covalent geometry : angle 0.53019 (10065) hydrogen bonds : bond 0.03378 ( 593) hydrogen bonds : angle 3.64894 ( 1773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1660.54 seconds wall clock time: 29 minutes 8.71 seconds (1748.71 seconds total)