Starting phenix.real_space_refine on Thu Jul 2 05:32:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wq0_66156/07_2026/9wq0_66156.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wq0_66156/07_2026/9wq0_66156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wq0_66156/07_2026/9wq0_66156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wq0_66156/07_2026/9wq0_66156.map" model { file = "/net/cci-nas-00/data/ceres_data/9wq0_66156/07_2026/9wq0_66156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wq0_66156/07_2026/9wq0_66156.cif" } resolution = 2.68 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= 0.102 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 P 6 5.49 5 S 54 5.16 5 C 4672 2.51 5 N 978 2.21 5 O 1108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6818 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2542 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 19, 'TRANS': 307} Chain: "B" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 426 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "C" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2542 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 19, 'TRANS': 307} Chain: "A" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 441 Unusual residues: {'3WF': 2, 'CLR': 5, 'PLM': 7, 'POV': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PLM:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 441 Unusual residues: {'3WF': 2, 'CLR': 5, 'PLM': 7, 'POV': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PLM:plan-1': 7} Unresolved non-hydrogen planarities: 7 Restraints were copied for chains: D Time building chain proxies: 1.81, per 1000 atoms: 0.27 Number of scatterers: 6818 At special positions: 0 Unit cell: (89.1, 89.1, 92.4, 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) S 54 16.00 P 6 15.00 O 1108 8.00 N 978 7.00 C 4672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 284 " distance=2.04 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=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 328.7 milliseconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1436 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 77.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.853A pdb=" N LEU A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 33 removed outlier: 3.673A pdb=" N CYS A 32 " --> pdb=" O PRO A 29 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 33 " --> pdb=" O SER A 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 29 through 33' Processing helix chain 'A' and resid 38 through 44 removed outlier: 3.707A pdb=" N ARG A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 79 Processing helix chain 'A' and resid 81 through 93 removed outlier: 3.513A pdb=" N THR A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 111 through 139 removed outlier: 4.110A pdb=" N TYR A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 173 through 202 Proline residue: A 184 - end of helix removed outlier: 3.899A pdb=" N TYR A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 247 removed outlier: 3.684A pdb=" N TRP A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 280 removed outlier: 4.118A pdb=" N GLN A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 289 through 318 removed outlier: 3.825A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 28 Processing helix chain 'B' and resid 33 through 68 Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.852A pdb=" N LEU C 19 " --> pdb=" O THR C 15 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL C 21 " --> pdb=" O ASP C 17 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY C 27 " --> pdb=" O LYS C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 33 removed outlier: 3.673A pdb=" N CYS C 32 " --> pdb=" O PRO C 29 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE C 33 " --> pdb=" O SER C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 29 through 33' Processing helix chain 'C' and resid 38 through 44 removed outlier: 3.706A pdb=" N ARG C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 79 Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.513A pdb=" N THR C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 108 Processing helix chain 'C' and resid 111 through 139 removed outlier: 4.110A pdb=" N TYR C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 148 Processing helix chain 'C' and resid 173 through 202 Proline residue: C 184 - end of helix removed outlier: 3.899A pdb=" N TYR C 187 " --> pdb=" O GLY C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 247 removed outlier: 3.684A pdb=" N TRP C 220 " --> pdb=" O SER C 216 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 280 removed outlier: 4.118A pdb=" N GLN C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Proline residue: C 270 - end of helix Processing helix chain 'C' and resid 289 through 318 removed outlier: 3.825A pdb=" N LEU C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 33 through 68 438 hydrogen bonds defined for protein. 1314 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: 0.93 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1059 1.33 - 1.45: 1532 1.45 - 1.57: 4285 1.57 - 1.70: 12 1.70 - 1.82: 80 Bond restraints: 6968 Sorted by residual: bond pdb=" N ILE D 40 " pdb=" CA ILE D 40 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.30e-02 5.92e+03 8.94e+00 bond pdb=" N ILE B 40 " pdb=" CA ILE B 40 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.30e-02 5.92e+03 8.79e+00 bond pdb=" N ILE B 49 " pdb=" CA ILE B 49 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.33e+00 bond pdb=" N ILE D 49 " pdb=" CA ILE D 49 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.30e+00 bond pdb=" N PRO C 165 " pdb=" CD PRO C 165 " ideal model delta sigma weight residual 1.473 1.501 -0.028 1.40e-02 5.10e+03 3.95e+00 ... (remaining 6963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 9001 1.48 - 2.96: 341 2.96 - 4.43: 32 4.43 - 5.91: 12 5.91 - 7.39: 10 Bond angle restraints: 9396 Sorted by residual: angle pdb=" C GLY A 248 " pdb=" N GLU A 249 " pdb=" CA GLU A 249 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C GLY C 248 " pdb=" N GLU C 249 " pdb=" CA GLU C 249 " ideal model delta sigma weight residual 121.54 128.22 -6.68 1.91e+00 2.74e-01 1.22e+01 angle pdb=" CA ILE D 49 " pdb=" C ILE D 49 " pdb=" O ILE D 49 " ideal model delta sigma weight residual 121.17 117.70 3.47 1.06e+00 8.90e-01 1.07e+01 angle pdb=" CA ILE B 49 " pdb=" C ILE B 49 " pdb=" O ILE B 49 " ideal model delta sigma weight residual 121.17 117.73 3.44 1.06e+00 8.90e-01 1.05e+01 angle pdb=" C LEU C 201 " pdb=" N VAL C 202 " pdb=" CA VAL C 202 " ideal model delta sigma weight residual 120.33 122.77 -2.44 8.00e-01 1.56e+00 9.32e+00 ... (remaining 9391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 4267 15.36 - 30.72: 439 30.72 - 46.09: 154 46.09 - 61.45: 54 61.45 - 76.81: 4 Dihedral angle restraints: 4918 sinusoidal: 2702 harmonic: 2216 Sorted by residual: dihedral pdb=" CG ARG A 85 " pdb=" CD ARG A 85 " pdb=" NE ARG A 85 " pdb=" CZ ARG A 85 " ideal model delta sinusoidal sigma weight residual 180.00 135.81 44.19 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG C 85 " pdb=" CD ARG C 85 " pdb=" NE ARG C 85 " pdb=" CZ ARG C 85 " ideal model delta sinusoidal sigma weight residual 180.00 135.82 44.18 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG C 146 " pdb=" CD ARG C 146 " pdb=" NE ARG C 146 " pdb=" CZ ARG C 146 " ideal model delta sinusoidal sigma weight residual -180.00 -136.39 -43.61 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 4915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 860 0.044 - 0.089: 192 0.089 - 0.133: 46 0.133 - 0.177: 4 0.177 - 0.222: 4 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CA MET C 154 " pdb=" N MET C 154 " pdb=" C MET C 154 " pdb=" CB MET C 154 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA MET A 154 " pdb=" N MET A 154 " pdb=" C MET A 154 " pdb=" CB MET A 154 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA GLU A 305 " pdb=" N GLU A 305 " pdb=" C GLU A 305 " pdb=" CB GLU A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.79e-01 ... (remaining 1103 not shown) Planarity restraints: 1028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 164 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO C 165 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 165 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 165 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 164 " 0.048 5.00e-02 4.00e+02 7.26e-02 8.44e+00 pdb=" N PRO A 165 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 117 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C MET A 117 " -0.038 2.00e-02 2.50e+03 pdb=" O MET A 117 " 0.014 2.00e-02 2.50e+03 pdb=" N THR A 118 " 0.013 2.00e-02 2.50e+03 ... (remaining 1025 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 980 2.77 - 3.30: 6037 3.30 - 3.83: 10268 3.83 - 4.37: 12441 4.37 - 4.90: 21983 Nonbonded interactions: 51709 Sorted by model distance: nonbonded pdb=" O SER A 30 " pdb=" OG SER A 34 " model vdw 2.232 3.040 nonbonded pdb=" O SER C 30 " pdb=" OG SER C 34 " model vdw 2.232 3.040 nonbonded pdb=" O LEU C 75 " pdb=" OG1 THR C 79 " model vdw 2.334 3.040 nonbonded pdb=" O LEU A 75 " pdb=" OG1 THR A 79 " model vdw 2.334 3.040 nonbonded pdb=" O LEU A 225 " pdb=" OG1 THR A 229 " model vdw 2.343 3.040 ... (remaining 51704 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 401 or resid 403 through 404 or resid 407 throug \ h 411)) selection = (chain 'C' and (resid 2 through 401 or resid 403 through 404 or resid 407 throug \ h 411)) } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.560 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.640 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.005 0.047 6984 Z= 0.249 Angle : 0.675 7.388 9400 Z= 0.378 Chirality : 0.041 0.222 1106 Planarity : 0.007 0.073 1028 Dihedral : 14.086 76.812 3476 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 18.07 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.30), residues: 752 helix: 2.21 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -2.27 (0.41), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 174 TYR 0.010 0.002 TYR A 187 PHE 0.016 0.002 PHE C 127 TRP 0.010 0.001 TRP C 220 HIS 0.009 0.002 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.25 ( 6968) covalent geometry : angle 0.67465 / 0.38 ( 9396) SS BOND : bond 0.00525 / 0.26 ( 2) SS BOND : angle 1.25036 / 0.66 ( 4) hydrogen bonds : bond 0.12737 / 8.36 ( 438) hydrogen bonds : angle 5.15160 / 3.67 ( 1314) Misc. bond : bond 0.00082 / 0.05 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.263 Fit side-chains REVERT: A 7 GLN cc_start: 0.6824 (pt0) cc_final: 0.6612 (mm110) REVERT: A 35 GLN cc_start: 0.7524 (mm-40) cc_final: 0.6940 (pp30) REVERT: A 154 MET cc_start: 0.7126 (mtm) cc_final: 0.6661 (mtm) REVERT: A 323 LYS cc_start: 0.8018 (mtmt) cc_final: 0.7283 (ptmm) REVERT: A 327 GLU cc_start: 0.7318 (tt0) cc_final: 0.6978 (tm-30) REVERT: B 24 MET cc_start: 0.6779 (mtp) cc_final: 0.6297 (mmm) REVERT: C 7 GLN cc_start: 0.6681 (pt0) cc_final: 0.6468 (mm110) REVERT: C 35 GLN cc_start: 0.7506 (mm-40) cc_final: 0.6924 (pp30) REVERT: C 154 MET cc_start: 0.7153 (mtm) cc_final: 0.6666 (mtm) REVERT: C 323 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7178 (ptmm) REVERT: C 327 GLU cc_start: 0.7319 (tt0) cc_final: 0.6997 (tm-30) REVERT: D 24 MET cc_start: 0.7012 (mtp) cc_final: 0.6447 (mmm) outliers start: 0 outliers final: 2 residues processed: 95 average time/residue: 0.5037 time to fit residues: 50.5568 Evaluate side-chains 91 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain D residue 40 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 GLN A 269 GLN A 300 HIS A 322 HIS C 260 GLN C 269 GLN C 300 HIS C 322 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.189352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.149580 restraints weight = 6929.539| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.42 r_work: 0.3561 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6984 Z= 0.158 Angle : 0.548 5.968 9400 Z= 0.278 Chirality : 0.038 0.133 1106 Planarity : 0.005 0.051 1028 Dihedral : 10.070 59.993 2072 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.56 % Allowed : 15.36 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.30), residues: 752 helix: 2.64 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -2.10 (0.40), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 314 TYR 0.013 0.002 TYR A 123 PHE 0.013 0.002 PHE C 138 TRP 0.012 0.002 TRP A 220 HIS 0.004 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 6968) covalent geometry : angle 0.54744 / 0.28 ( 9396) SS BOND : bond 0.00573 / 0.29 ( 2) SS BOND : angle 1.51441 / 0.84 ( 4) hydrogen bonds : bond 0.06583 / 4.36 ( 438) hydrogen bonds : angle 3.75303 / 2.71 ( 1314) Misc. bond : bond 0.00037 / 0.02 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.6736 (pt0) cc_final: 0.6309 (mm110) REVERT: A 35 GLN cc_start: 0.7617 (mm-40) cc_final: 0.6742 (pp30) REVERT: A 142 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7215 (mm-30) REVERT: A 309 MET cc_start: 0.8486 (mmp) cc_final: 0.8276 (mmp) REVERT: A 323 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7104 (ptmm) REVERT: A 327 GLU cc_start: 0.7354 (tt0) cc_final: 0.6702 (tm-30) REVERT: B 24 MET cc_start: 0.6176 (mtp) cc_final: 0.5693 (mmm) REVERT: C 7 GLN cc_start: 0.6596 (pt0) cc_final: 0.6208 (mm110) REVERT: C 35 GLN cc_start: 0.7632 (mm-40) cc_final: 0.6682 (pp30) REVERT: C 154 MET cc_start: 0.7567 (mtm) cc_final: 0.6948 (mtm) REVERT: C 323 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7052 (ptmm) REVERT: C 327 GLU cc_start: 0.7419 (tt0) cc_final: 0.6755 (tm-30) REVERT: D 24 MET cc_start: 0.6324 (mtp) cc_final: 0.5745 (mmm) outliers start: 17 outliers final: 8 residues processed: 100 average time/residue: 0.4702 time to fit residues: 49.9822 Evaluate side-chains 101 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 49 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 56 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 GLN A 322 HIS C 260 GLN C 322 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.189600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149617 restraints weight = 6862.787| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.42 r_work: 0.3612 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6984 Z= 0.142 Angle : 0.537 10.311 9400 Z= 0.272 Chirality : 0.037 0.241 1106 Planarity : 0.005 0.052 1028 Dihedral : 9.979 59.946 2072 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.41 % Allowed : 17.32 % Favored : 80.27 % 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: 2.57 (0.30), residues: 752 helix: 2.74 (0.20), residues: 574 sheet: None (None), residues: 0 loop : -2.05 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 110 TYR 0.015 0.002 TYR A 123 PHE 0.015 0.002 PHE A 127 TRP 0.009 0.001 TRP A 220 HIS 0.011 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 6968) covalent geometry : angle 0.53579 / 0.27 ( 9396) SS BOND : bond 0.01143 / 0.55 ( 2) SS BOND : angle 1.76430 / 0.92 ( 4) hydrogen bonds : bond 0.06289 / 4.19 ( 438) hydrogen bonds : angle 3.66709 / 2.64 ( 1314) Misc. bond : bond 0.00027 / 0.02 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.6778 (pt0) cc_final: 0.6376 (mm110) REVERT: A 35 GLN cc_start: 0.7704 (mm-40) cc_final: 0.6883 (pp30) REVERT: A 142 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7328 (mm-30) REVERT: A 309 MET cc_start: 0.8538 (mmp) cc_final: 0.8203 (mmt) REVERT: A 323 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7193 (ptmm) REVERT: A 327 GLU cc_start: 0.7331 (tt0) cc_final: 0.6721 (tm-30) REVERT: B 24 MET cc_start: 0.6160 (mtp) cc_final: 0.5723 (mmm) REVERT: C 7 GLN cc_start: 0.6621 (pt0) cc_final: 0.6271 (mm110) REVERT: C 35 GLN cc_start: 0.7691 (mm-40) cc_final: 0.6805 (pp30) REVERT: C 154 MET cc_start: 0.7645 (mtm) cc_final: 0.7055 (mtm) REVERT: C 169 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.5978 (mmm-85) REVERT: C 323 LYS cc_start: 0.8041 (mtmt) cc_final: 0.7152 (ptmm) REVERT: C 327 GLU cc_start: 0.7443 (tt0) cc_final: 0.6854 (tm-30) REVERT: D 24 MET cc_start: 0.6371 (mtp) cc_final: 0.5777 (mmm) outliers start: 16 outliers final: 9 residues processed: 97 average time/residue: 0.5377 time to fit residues: 55.1235 Evaluate side-chains 100 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 169 ARG Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 49 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 0.0370 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 GLN A 322 HIS C 260 GLN C 322 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.190120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150247 restraints weight = 6880.980| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.41 r_work: 0.3578 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6984 Z= 0.131 Angle : 0.523 7.673 9400 Z= 0.266 Chirality : 0.036 0.174 1106 Planarity : 0.005 0.055 1028 Dihedral : 9.899 59.733 2068 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.81 % Allowed : 18.52 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.30), residues: 752 helix: 2.76 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -1.95 (0.41), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 241 TYR 0.015 0.001 TYR A 123 PHE 0.014 0.002 PHE C 127 TRP 0.008 0.001 TRP A 220 HIS 0.015 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 ( 6968) covalent geometry : angle 0.52232 / 0.27 ( 9396) SS BOND : bond 0.01158 / 0.56 ( 2) SS BOND : angle 0.97306 / 0.51 ( 4) hydrogen bonds : bond 0.06047 / 4.02 ( 438) hydrogen bonds : angle 3.64552 / 2.63 ( 1314) Misc. bond : bond 0.00018 / 0.01 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.236 Fit side-chains REVERT: A 7 GLN cc_start: 0.6740 (pt0) cc_final: 0.6325 (mm110) REVERT: A 35 GLN cc_start: 0.7659 (mm-40) cc_final: 0.6816 (pp30) REVERT: A 142 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7271 (mm-30) REVERT: A 309 MET cc_start: 0.8518 (mmp) cc_final: 0.8294 (mmp) REVERT: A 323 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7169 (ptmm) REVERT: A 327 GLU cc_start: 0.7318 (tt0) cc_final: 0.6692 (tm-30) REVERT: B 24 MET cc_start: 0.6035 (mtp) cc_final: 0.5575 (mmm) REVERT: C 7 GLN cc_start: 0.6596 (pt0) cc_final: 0.6228 (mm110) REVERT: C 35 GLN cc_start: 0.7638 (mm-40) cc_final: 0.6722 (pp30) REVERT: C 154 MET cc_start: 0.7618 (mtm) cc_final: 0.7009 (mtm) REVERT: C 323 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7118 (ptmm) REVERT: C 327 GLU cc_start: 0.7408 (tt0) cc_final: 0.6805 (tm-30) REVERT: D 24 MET cc_start: 0.6318 (mtp) cc_final: 0.5733 (mmm) outliers start: 12 outliers final: 10 residues processed: 95 average time/residue: 0.5087 time to fit residues: 51.0296 Evaluate side-chains 99 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 49 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 156 HIS ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS C 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.190150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.150115 restraints weight = 6903.201| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.42 r_work: 0.3579 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6984 Z= 0.132 Angle : 0.522 7.674 9400 Z= 0.265 Chirality : 0.036 0.174 1106 Planarity : 0.006 0.069 1028 Dihedral : 9.897 59.733 2068 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.51 % Allowed : 18.67 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.30), residues: 752 helix: 2.76 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -1.95 (0.41), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 241 TYR 0.015 0.001 TYR A 123 PHE 0.014 0.002 PHE C 127 TRP 0.008 0.001 TRP A 220 HIS 0.015 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 6968) covalent geometry : angle 0.52135 / 0.27 ( 9396) SS BOND : bond 0.01158 / 0.56 ( 2) SS BOND : angle 0.97306 / 0.51 ( 4) hydrogen bonds : bond 0.06048 / 4.02 ( 438) hydrogen bonds : angle 3.64551 / 2.63 ( 1314) Misc. bond : bond 0.00018 / 0.01 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.245 Fit side-chains REVERT: A 7 GLN cc_start: 0.6722 (pt0) cc_final: 0.6304 (mm110) REVERT: A 35 GLN cc_start: 0.7636 (mm-40) cc_final: 0.6769 (pp30) REVERT: A 142 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7238 (mm-30) REVERT: A 309 MET cc_start: 0.8486 (mmp) cc_final: 0.8259 (mmp) REVERT: A 323 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7137 (ptmm) REVERT: A 327 GLU cc_start: 0.7298 (tt0) cc_final: 0.6653 (tm-30) REVERT: B 24 MET cc_start: 0.6015 (mtp) cc_final: 0.5555 (mmm) REVERT: C 7 GLN cc_start: 0.6589 (pt0) cc_final: 0.6215 (mm110) REVERT: C 35 GLN cc_start: 0.7620 (mm-40) cc_final: 0.6686 (pp30) REVERT: C 154 MET cc_start: 0.7606 (mtm) cc_final: 0.6985 (mtm) REVERT: C 323 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7077 (ptmm) REVERT: C 327 GLU cc_start: 0.7390 (tt0) cc_final: 0.6776 (tm-30) REVERT: D 24 MET cc_start: 0.6297 (mtp) cc_final: 0.5710 (mmm) outliers start: 10 outliers final: 10 residues processed: 92 average time/residue: 0.5359 time to fit residues: 52.0078 Evaluate side-chains 99 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 49 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.190150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.150100 restraints weight = 6906.721| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.42 r_work: 0.3579 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6984 Z= 0.132 Angle : 0.522 7.674 9400 Z= 0.265 Chirality : 0.036 0.174 1106 Planarity : 0.006 0.069 1028 Dihedral : 9.897 59.733 2068 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.51 % Allowed : 18.67 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.30), residues: 752 helix: 2.76 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -1.95 (0.41), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 241 TYR 0.015 0.001 TYR A 123 PHE 0.014 0.002 PHE C 127 TRP 0.008 0.001 TRP A 220 HIS 0.015 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 6968) covalent geometry : angle 0.52135 / 0.27 ( 9396) SS BOND : bond 0.01158 / 0.56 ( 2) SS BOND : angle 0.97306 / 0.51 ( 4) hydrogen bonds : bond 0.06048 / 4.02 ( 438) hydrogen bonds : angle 3.64551 / 2.63 ( 1314) Misc. bond : bond 0.00018 / 0.01 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.237 Fit side-chains REVERT: A 7 GLN cc_start: 0.6721 (pt0) cc_final: 0.6300 (mm110) REVERT: A 35 GLN cc_start: 0.7635 (mm-40) cc_final: 0.6767 (pp30) REVERT: A 142 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7239 (mm-30) REVERT: A 309 MET cc_start: 0.8489 (mmp) cc_final: 0.8262 (mmp) REVERT: A 323 LYS cc_start: 0.8072 (mtmt) cc_final: 0.7137 (ptmm) REVERT: A 327 GLU cc_start: 0.7299 (tt0) cc_final: 0.6654 (tm-30) REVERT: B 24 MET cc_start: 0.6007 (mtp) cc_final: 0.5547 (mmm) REVERT: C 7 GLN cc_start: 0.6587 (pt0) cc_final: 0.6211 (mm110) REVERT: C 35 GLN cc_start: 0.7621 (mm-40) cc_final: 0.6686 (pp30) REVERT: C 154 MET cc_start: 0.7608 (mtm) cc_final: 0.6986 (mtm) REVERT: C 323 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7078 (ptmm) REVERT: C 327 GLU cc_start: 0.7391 (tt0) cc_final: 0.6778 (tm-30) REVERT: D 24 MET cc_start: 0.6289 (mtp) cc_final: 0.5701 (mmm) outliers start: 10 outliers final: 10 residues processed: 92 average time/residue: 0.5333 time to fit residues: 51.7683 Evaluate side-chains 99 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 49 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.0370 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.190150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150162 restraints weight = 6845.297| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.41 r_work: 0.3580 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6984 Z= 0.132 Angle : 0.522 7.674 9400 Z= 0.265 Chirality : 0.036 0.174 1106 Planarity : 0.006 0.069 1028 Dihedral : 9.897 59.733 2068 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.51 % Allowed : 18.67 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.30), residues: 752 helix: 2.76 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -1.95 (0.41), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 241 TYR 0.015 0.001 TYR A 123 PHE 0.014 0.002 PHE C 127 TRP 0.008 0.001 TRP A 220 HIS 0.015 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 6968) covalent geometry : angle 0.52135 / 0.27 ( 9396) SS BOND : bond 0.01158 / 0.56 ( 2) SS BOND : angle 0.97306 / 0.51 ( 4) hydrogen bonds : bond 0.06048 / 4.02 ( 438) hydrogen bonds : angle 3.64551 / 2.63 ( 1314) Misc. bond : bond 0.00018 / 0.01 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.255 Fit side-chains REVERT: A 7 GLN cc_start: 0.6723 (pt0) cc_final: 0.6307 (mm110) REVERT: A 35 GLN cc_start: 0.7636 (mm-40) cc_final: 0.6769 (pp30) REVERT: A 142 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7238 (mm-30) REVERT: A 309 MET cc_start: 0.8486 (mmp) cc_final: 0.8258 (mmp) REVERT: A 323 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7136 (ptmm) REVERT: A 327 GLU cc_start: 0.7296 (tt0) cc_final: 0.6652 (tm-30) REVERT: B 24 MET cc_start: 0.6021 (mtp) cc_final: 0.5562 (mmm) REVERT: C 7 GLN cc_start: 0.6589 (pt0) cc_final: 0.6217 (mm110) REVERT: C 35 GLN cc_start: 0.7620 (mm-40) cc_final: 0.6687 (pp30) REVERT: C 154 MET cc_start: 0.7604 (mtm) cc_final: 0.6982 (mtm) REVERT: C 323 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7077 (ptmm) REVERT: C 327 GLU cc_start: 0.7389 (tt0) cc_final: 0.6776 (tm-30) REVERT: D 24 MET cc_start: 0.6304 (mtp) cc_final: 0.5716 (mmm) outliers start: 10 outliers final: 10 residues processed: 92 average time/residue: 0.5136 time to fit residues: 49.8925 Evaluate side-chains 99 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 49 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.190150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.150138 restraints weight = 6880.344| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.42 r_work: 0.3578 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6984 Z= 0.132 Angle : 0.522 7.674 9400 Z= 0.265 Chirality : 0.036 0.174 1106 Planarity : 0.006 0.069 1028 Dihedral : 9.897 59.733 2068 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.51 % Allowed : 18.67 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.30), residues: 752 helix: 2.76 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -1.95 (0.41), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 241 TYR 0.015 0.001 TYR A 123 PHE 0.014 0.002 PHE C 127 TRP 0.008 0.001 TRP A 220 HIS 0.015 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 6968) covalent geometry : angle 0.52135 / 0.27 ( 9396) SS BOND : bond 0.01158 / 0.56 ( 2) SS BOND : angle 0.97306 / 0.51 ( 4) hydrogen bonds : bond 0.06048 / 4.02 ( 438) hydrogen bonds : angle 3.64551 / 2.63 ( 1314) Misc. bond : bond 0.00018 / 0.01 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.416 Fit side-chains REVERT: A 7 GLN cc_start: 0.6741 (pt0) cc_final: 0.6334 (mm110) REVERT: A 35 GLN cc_start: 0.7660 (mm-40) cc_final: 0.6813 (pp30) REVERT: A 142 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7271 (mm-30) REVERT: A 309 MET cc_start: 0.8511 (mmp) cc_final: 0.8289 (mmp) REVERT: A 323 LYS cc_start: 0.8092 (mtmt) cc_final: 0.7164 (ptmm) REVERT: A 327 GLU cc_start: 0.7308 (tt0) cc_final: 0.6676 (tm-30) REVERT: B 24 MET cc_start: 0.6056 (mtp) cc_final: 0.5600 (mmm) REVERT: C 7 GLN cc_start: 0.6606 (pt0) cc_final: 0.6243 (mm110) REVERT: C 35 GLN cc_start: 0.7643 (mm-40) cc_final: 0.6731 (pp30) REVERT: C 154 MET cc_start: 0.7618 (mtm) cc_final: 0.7009 (mtm) REVERT: C 323 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7106 (ptmm) REVERT: C 327 GLU cc_start: 0.7400 (tt0) cc_final: 0.6798 (tm-30) REVERT: D 24 MET cc_start: 0.6347 (mtp) cc_final: 0.5762 (mmm) outliers start: 10 outliers final: 10 residues processed: 92 average time/residue: 0.5642 time to fit residues: 54.7603 Evaluate side-chains 99 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 49 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.190150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.150080 restraints weight = 6918.024| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.42 r_work: 0.3579 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6984 Z= 0.132 Angle : 0.522 7.674 9400 Z= 0.265 Chirality : 0.036 0.174 1106 Planarity : 0.006 0.069 1028 Dihedral : 9.897 59.733 2068 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.51 % Allowed : 18.67 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.30), residues: 752 helix: 2.76 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -1.95 (0.41), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 241 TYR 0.015 0.001 TYR A 123 PHE 0.014 0.002 PHE C 127 TRP 0.008 0.001 TRP A 220 HIS 0.015 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 6968) covalent geometry : angle 0.52135 / 0.27 ( 9396) SS BOND : bond 0.01158 / 0.56 ( 2) SS BOND : angle 0.97306 / 0.51 ( 4) hydrogen bonds : bond 0.06048 / 4.02 ( 438) hydrogen bonds : angle 3.64551 / 2.63 ( 1314) Misc. bond : bond 0.00018 / 0.01 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.275 Fit side-chains REVERT: A 7 GLN cc_start: 0.6722 (pt0) cc_final: 0.6302 (mm110) REVERT: A 35 GLN cc_start: 0.7635 (mm-40) cc_final: 0.6767 (pp30) REVERT: A 142 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7240 (mm-30) REVERT: A 309 MET cc_start: 0.8488 (mmp) cc_final: 0.8260 (mmp) REVERT: A 323 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7137 (ptmm) REVERT: A 327 GLU cc_start: 0.7299 (tt0) cc_final: 0.6653 (tm-30) REVERT: B 24 MET cc_start: 0.6008 (mtp) cc_final: 0.5548 (mmm) REVERT: C 7 GLN cc_start: 0.6588 (pt0) cc_final: 0.6212 (mm110) REVERT: C 35 GLN cc_start: 0.7621 (mm-40) cc_final: 0.6685 (pp30) REVERT: C 154 MET cc_start: 0.7608 (mtm) cc_final: 0.6987 (mtm) REVERT: C 323 LYS cc_start: 0.7987 (mtmt) cc_final: 0.7077 (ptmm) REVERT: C 327 GLU cc_start: 0.7391 (tt0) cc_final: 0.6777 (tm-30) REVERT: D 24 MET cc_start: 0.6291 (mtp) cc_final: 0.5703 (mmm) outliers start: 10 outliers final: 10 residues processed: 92 average time/residue: 0.5498 time to fit residues: 53.3041 Evaluate side-chains 99 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 49 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.190150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.150097 restraints weight = 6897.159| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.42 r_work: 0.3579 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6984 Z= 0.132 Angle : 0.522 7.674 9400 Z= 0.265 Chirality : 0.036 0.174 1106 Planarity : 0.006 0.069 1028 Dihedral : 9.897 59.733 2068 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.51 % Allowed : 18.67 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.30), residues: 752 helix: 2.76 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -1.95 (0.41), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 241 TYR 0.015 0.001 TYR A 123 PHE 0.014 0.002 PHE C 127 TRP 0.008 0.001 TRP A 220 HIS 0.015 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 6968) covalent geometry : angle 0.52135 / 0.27 ( 9396) SS BOND : bond 0.01158 / 0.56 ( 2) SS BOND : angle 0.97306 / 0.51 ( 4) hydrogen bonds : bond 0.06048 / 4.02 ( 438) hydrogen bonds : angle 3.64551 / 2.63 ( 1314) Misc. bond : bond 0.00018 / 0.01 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.243 Fit side-chains REVERT: A 7 GLN cc_start: 0.6722 (pt0) cc_final: 0.6307 (mm110) REVERT: A 35 GLN cc_start: 0.7637 (mm-40) cc_final: 0.6770 (pp30) REVERT: A 142 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7239 (mm-30) REVERT: A 309 MET cc_start: 0.8487 (mmp) cc_final: 0.8260 (mmp) REVERT: A 323 LYS cc_start: 0.8074 (mtmt) cc_final: 0.7136 (ptmm) REVERT: A 327 GLU cc_start: 0.7297 (tt0) cc_final: 0.6651 (tm-30) REVERT: B 24 MET cc_start: 0.6024 (mtp) cc_final: 0.5565 (mmm) REVERT: C 7 GLN cc_start: 0.6589 (pt0) cc_final: 0.6218 (mm110) REVERT: C 35 GLN cc_start: 0.7621 (mm-40) cc_final: 0.6688 (pp30) REVERT: C 154 MET cc_start: 0.7605 (mtm) cc_final: 0.6982 (mtm) REVERT: C 323 LYS cc_start: 0.7990 (mtmt) cc_final: 0.7077 (ptmm) REVERT: C 327 GLU cc_start: 0.7389 (tt0) cc_final: 0.6775 (tm-30) REVERT: D 24 MET cc_start: 0.6311 (mtp) cc_final: 0.5722 (mmm) outliers start: 10 outliers final: 10 residues processed: 92 average time/residue: 0.5616 time to fit residues: 54.5656 Evaluate side-chains 99 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 49 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.190150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150165 restraints weight = 6860.414| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.41 r_work: 0.3579 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6984 Z= 0.132 Angle : 0.522 7.674 9400 Z= 0.265 Chirality : 0.036 0.174 1106 Planarity : 0.006 0.069 1028 Dihedral : 9.897 59.733 2068 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.51 % Allowed : 18.67 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.30), residues: 752 helix: 2.76 (0.20), residues: 576 sheet: None (None), residues: 0 loop : -1.95 (0.41), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 241 TYR 0.015 0.001 TYR A 123 PHE 0.014 0.002 PHE C 127 TRP 0.008 0.001 TRP A 220 HIS 0.015 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 6968) covalent geometry : angle 0.52135 / 0.27 ( 9396) SS BOND : bond 0.01158 / 0.56 ( 2) SS BOND : angle 0.97306 / 0.51 ( 4) hydrogen bonds : bond 0.06048 / 4.02 ( 438) hydrogen bonds : angle 3.64551 / 2.63 ( 1314) Misc. bond : bond 0.00018 / 0.01 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2347.18 seconds wall clock time: 40 minutes 50.43 seconds (2450.43 seconds total)