Starting phenix.real_space_refine on Sun Apr 5 05:07:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u67_63898/04_2026/9u67_63898.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u67_63898/04_2026/9u67_63898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u67_63898/04_2026/9u67_63898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u67_63898/04_2026/9u67_63898.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u67_63898/04_2026/9u67_63898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u67_63898/04_2026/9u67_63898.map" } resolution = 3.32 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= 0.028 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 5175 2.51 5 N 1416 2.21 5 O 1557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8184 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2251 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain: "F" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 477 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "A" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2251 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain: "B" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 477 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "C" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2251 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain: "D" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 477 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Time building chain proxies: 1.80, per 1000 atoms: 0.22 Number of scatterers: 8184 At special positions: 0 Unit cell: (88.56, 86.1, 107.42, 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 1557 8.00 N 1416 7.00 C 5175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS E 90 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 279 " - pdb=" SG CYS E 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 303 " distance=2.03 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: 0.79 Conformation dependent library (CDL) restraints added in 305.6 milliseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 19 sheets defined 21.6% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'E' and resid 56 through 63 Processing helix chain 'E' and resid 97 through 105 Processing helix chain 'E' and resid 118 through 123 removed outlier: 4.256A pdb=" N TRP E 123 " --> pdb=" O LYS E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 192 removed outlier: 3.813A pdb=" N GLN E 188 " --> pdb=" O THR E 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 58 Processing helix chain 'F' and resid 74 through 109 Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 118 through 123 removed outlier: 4.247A pdb=" N TRP A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 removed outlier: 3.627A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 74 through 109 Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 118 through 123 removed outlier: 4.272A pdb=" N TRP C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 192 removed outlier: 3.736A pdb=" N GLN C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'D' and resid 74 through 109 Processing sheet with id=AA1, first strand: chain 'E' and resid 41 through 43 removed outlier: 6.225A pdb=" N LEU E 41 " --> pdb=" O HIS E 273 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N CYS E 275 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 50 through 51 removed outlier: 6.800A pdb=" N LEU E 50 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 108 through 114 removed outlier: 6.890A pdb=" N LYS E 258 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE E 111 " --> pdb=" O ALA E 256 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA E 256 " --> pdb=" O PHE E 111 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG E 113 " --> pdb=" O ALA E 254 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA E 254 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU E 172 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 148 through 150 Processing sheet with id=AA5, first strand: chain 'E' and resid 162 through 166 Processing sheet with id=AA6, first strand: chain 'E' and resid 280 through 281 Processing sheet with id=AA7, first strand: chain 'E' and resid 292 through 293 Processing sheet with id=AA8, first strand: chain 'A' and resid 41 through 43 removed outlier: 6.032A pdb=" N LEU A 41 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N CYS A 275 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 50 through 51 removed outlier: 6.837A pdb=" N LEU A 50 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 108 through 115 removed outlier: 6.729A pdb=" N LYS A 258 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE A 111 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 256 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARG A 113 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA A 254 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N HIS A 253 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE A 176 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AB3, first strand: chain 'A' and resid 162 through 166 Processing sheet with id=AB4, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AB5, first strand: chain 'C' and resid 41 through 43 removed outlier: 6.221A pdb=" N LEU C 41 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N CYS C 275 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.759A pdb=" N LEU C 50 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 110 through 114 removed outlier: 3.947A pdb=" N SER C 110 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 258 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 148 through 150 Processing sheet with id=AB9, first strand: chain 'C' and resid 162 through 166 Processing sheet with id=AC1, first strand: chain 'C' and resid 280 through 281 248 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1350 1.31 - 1.44: 2303 1.44 - 1.57: 4675 1.57 - 1.69: 0 1.69 - 1.82: 48 Bond restraints: 8376 Sorted by residual: bond pdb=" C PRO A 297 " pdb=" O PRO A 297 " ideal model delta sigma weight residual 1.238 1.188 0.049 1.35e-02 5.49e+03 1.34e+01 bond pdb=" N PRO A 297 " pdb=" CA PRO A 297 " ideal model delta sigma weight residual 1.473 1.428 0.045 1.33e-02 5.65e+03 1.15e+01 bond pdb=" N PRO C 297 " pdb=" CA PRO C 297 " ideal model delta sigma weight residual 1.473 1.428 0.045 1.33e-02 5.65e+03 1.15e+01 bond pdb=" C PRO C 297 " pdb=" O PRO C 297 " ideal model delta sigma weight residual 1.238 1.197 0.041 1.35e-02 5.49e+03 9.13e+00 bond pdb=" N LYS C 259 " pdb=" CA LYS C 259 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.20e-02 6.94e+03 4.69e+00 ... (remaining 8371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 11194 2.08 - 4.16: 137 4.16 - 6.25: 23 6.25 - 8.33: 4 8.33 - 10.41: 3 Bond angle restraints: 11361 Sorted by residual: angle pdb=" CA PRO A 92 " pdb=" N PRO A 92 " pdb=" CD PRO A 92 " ideal model delta sigma weight residual 112.00 105.11 6.89 1.40e+00 5.10e-01 2.42e+01 angle pdb=" C PRO A 297 " pdb=" CA PRO A 297 " pdb=" CB PRO A 297 " ideal model delta sigma weight residual 113.20 105.07 8.13 1.69e+00 3.50e-01 2.32e+01 angle pdb=" C PRO C 297 " pdb=" CA PRO C 297 " pdb=" CB PRO C 297 " ideal model delta sigma weight residual 113.20 106.78 6.42 1.69e+00 3.50e-01 1.44e+01 angle pdb=" CA LEU A 161 " pdb=" CB LEU A 161 " pdb=" CG LEU A 161 " ideal model delta sigma weight residual 116.30 126.71 -10.41 3.50e+00 8.16e-02 8.85e+00 angle pdb=" CA LYS E 259 " pdb=" C LYS E 259 " pdb=" O LYS E 259 " ideal model delta sigma weight residual 120.40 117.72 2.68 1.05e+00 9.07e-01 6.53e+00 ... (remaining 11356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.30: 4491 15.30 - 30.60: 399 30.60 - 45.91: 112 45.91 - 61.21: 19 61.21 - 76.51: 4 Dihedral angle restraints: 5025 sinusoidal: 2031 harmonic: 2994 Sorted by residual: dihedral pdb=" CB CYS A 55 " pdb=" SG CYS A 55 " pdb=" SG CYS A 67 " pdb=" CB CYS A 67 " ideal model delta sinusoidal sigma weight residual -86.00 -136.93 50.93 1 1.00e+01 1.00e-02 3.55e+01 dihedral pdb=" CB CYS C 55 " pdb=" SG CYS C 55 " pdb=" SG CYS C 67 " pdb=" CB CYS C 67 " ideal model delta sinusoidal sigma weight residual -86.00 -135.60 49.60 1 1.00e+01 1.00e-02 3.38e+01 dihedral pdb=" CB CYS E 55 " pdb=" SG CYS E 55 " pdb=" SG CYS E 67 " pdb=" CB CYS E 67 " ideal model delta sinusoidal sigma weight residual -86.00 -134.12 48.12 1 1.00e+01 1.00e-02 3.19e+01 ... (remaining 5022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 838 0.035 - 0.071: 296 0.071 - 0.106: 75 0.106 - 0.142: 37 0.142 - 0.177: 2 Chirality restraints: 1248 Sorted by residual: chirality pdb=" CA LYS E 259 " pdb=" N LYS E 259 " pdb=" C LYS E 259 " pdb=" CB LYS E 259 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CA PRO A 92 " pdb=" N PRO A 92 " pdb=" C PRO A 92 " pdb=" CB PRO A 92 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CA ILE A 48 " pdb=" N ILE A 48 " pdb=" C ILE A 48 " pdb=" CB ILE A 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 1245 not shown) Planarity restraints: 1455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 91 " -0.080 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO A 92 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 91 " -0.045 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO E 92 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 92 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 92 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 258 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.34e+00 pdb=" C LYS E 258 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS E 258 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS E 259 " 0.015 2.00e-02 2.50e+03 ... (remaining 1452 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 574 2.74 - 3.28: 7683 3.28 - 3.82: 12942 3.82 - 4.36: 14856 4.36 - 4.90: 25975 Nonbonded interactions: 62030 Sorted by model distance: nonbonded pdb=" OE2 GLU A 172 " pdb=" NZ LYS A 259 " model vdw 2.196 3.120 nonbonded pdb=" NZ LYS C 102 " pdb=" OE1 GLU D 69 " model vdw 2.232 3.120 nonbonded pdb=" NZ LYS A 102 " pdb=" OE1 GLU B 69 " model vdw 2.248 3.120 nonbonded pdb=" NE1 TRP C 150 " pdb=" OH TYR C 192 " model vdw 2.252 3.120 nonbonded pdb=" O CYS E 42 " pdb=" OH TYR E 78 " model vdw 2.263 3.040 ... (remaining 62025 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' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.630 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8388 Z= 0.155 Angle : 0.620 10.411 11385 Z= 0.320 Chirality : 0.042 0.177 1248 Planarity : 0.005 0.117 1455 Dihedral : 12.760 76.510 3063 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.11 % Allowed : 0.54 % Favored : 99.35 % 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: -0.64 (0.26), residues: 1020 helix: 1.96 (0.37), residues: 210 sheet: 0.98 (0.37), residues: 204 loop : -1.95 (0.22), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.035 0.002 TYR A 91 PHE 0.011 0.001 PHE C 111 TRP 0.006 0.001 TRP B 92 HIS 0.002 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8376) covalent geometry : angle 0.61858 (11361) SS BOND : bond 0.00202 ( 12) SS BOND : angle 1.04830 ( 24) hydrogen bonds : bond 0.13618 ( 248) hydrogen bonds : angle 5.84642 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 61 ILE cc_start: 0.8571 (tp) cc_final: 0.8234 (tp) REVERT: E 66 LYS cc_start: 0.8531 (mmpt) cc_final: 0.8316 (mmpt) REVERT: E 100 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6951 (mm-30) REVERT: E 102 LYS cc_start: 0.8387 (mtpp) cc_final: 0.8172 (mtpt) REVERT: E 133 THR cc_start: 0.8587 (m) cc_final: 0.8366 (t) REVERT: E 161 LEU cc_start: 0.8744 (tp) cc_final: 0.8541 (tt) REVERT: E 205 LYS cc_start: 0.8308 (mtmm) cc_final: 0.8101 (mtmm) REVERT: E 265 ILE cc_start: 0.8567 (mm) cc_final: 0.8136 (mm) REVERT: E 266 MET cc_start: 0.6968 (tpp) cc_final: 0.6386 (tpp) REVERT: E 305 LYS cc_start: 0.8776 (tppp) cc_final: 0.8245 (tppp) REVERT: F 59 MET cc_start: 0.6525 (tpt) cc_final: 0.6071 (tpt) REVERT: F 100 ILE cc_start: 0.8680 (mp) cc_final: 0.8478 (mp) REVERT: F 106 ARG cc_start: 0.7698 (tmt-80) cc_final: 0.7460 (tmt-80) REVERT: A 40 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7879 (mtpp) REVERT: A 61 ILE cc_start: 0.8458 (tp) cc_final: 0.8048 (tp) REVERT: A 213 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7110 (mt-10) REVERT: A 299 THR cc_start: 0.7985 (p) cc_final: 0.7741 (p) REVERT: A 312 LEU cc_start: 0.8399 (tp) cc_final: 0.8038 (tp) REVERT: B 100 ILE cc_start: 0.8618 (mp) cc_final: 0.8402 (mp) REVERT: B 106 ARG cc_start: 0.7827 (tmt170) cc_final: 0.7421 (tmt170) REVERT: C 61 ILE cc_start: 0.8309 (tp) cc_final: 0.7903 (tp) REVERT: C 142 ASN cc_start: 0.8466 (m-40) cc_final: 0.8164 (m-40) REVERT: C 219 LYS cc_start: 0.8268 (mtpp) cc_final: 0.8027 (mtpp) REVERT: C 266 MET cc_start: 0.6923 (tpp) cc_final: 0.6490 (tpp) REVERT: D 106 ARG cc_start: 0.7928 (tpm170) cc_final: 0.7699 (tpm170) outliers start: 1 outliers final: 0 residues processed: 304 average time/residue: 0.0851 time to fit residues: 35.4714 Evaluate side-chains 285 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 293 GLN F 95 ASN A 74 ASN ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN C 54 ASN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN C 196 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.107437 restraints weight = 13037.859| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.89 r_work: 0.3205 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8388 Z= 0.154 Angle : 0.564 9.070 11385 Z= 0.282 Chirality : 0.041 0.129 1248 Planarity : 0.004 0.061 1455 Dihedral : 4.041 18.156 1101 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.18 % Allowed : 15.69 % Favored : 82.14 % 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: -0.43 (0.26), residues: 1020 helix: 2.03 (0.37), residues: 216 sheet: 1.06 (0.34), residues: 231 loop : -1.93 (0.23), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.022 0.002 TYR E 91 PHE 0.015 0.002 PHE C 111 TRP 0.010 0.001 TRP C 60 HIS 0.004 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8376) covalent geometry : angle 0.56124 (11361) SS BOND : bond 0.00289 ( 12) SS BOND : angle 1.41431 ( 24) hydrogen bonds : bond 0.03976 ( 248) hydrogen bonds : angle 4.57893 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 304 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 LYS cc_start: 0.7569 (mttt) cc_final: 0.7153 (mttt) REVERT: E 61 ILE cc_start: 0.8542 (tp) cc_final: 0.8193 (tp) REVERT: E 100 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7482 (mm-30) REVERT: E 133 THR cc_start: 0.8601 (m) cc_final: 0.8345 (t) REVERT: E 161 LEU cc_start: 0.8824 (tp) cc_final: 0.8609 (tt) REVERT: E 205 LYS cc_start: 0.8504 (mtmm) cc_final: 0.8231 (mtmm) REVERT: E 265 ILE cc_start: 0.8747 (mm) cc_final: 0.8323 (mm) REVERT: E 266 MET cc_start: 0.7672 (tpp) cc_final: 0.7180 (tpp) REVERT: F 100 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8627 (mp) REVERT: A 40 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8043 (mtpp) REVERT: A 57 VAL cc_start: 0.7686 (t) cc_final: 0.7295 (p) REVERT: A 61 ILE cc_start: 0.8457 (tp) cc_final: 0.8206 (tp) REVERT: A 142 ASN cc_start: 0.8416 (m-40) cc_final: 0.8210 (m-40) REVERT: A 213 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7639 (mt-10) REVERT: A 223 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7806 (mm-40) REVERT: A 247 ASN cc_start: 0.7194 (m110) cc_final: 0.6897 (m110) REVERT: A 266 MET cc_start: 0.7785 (tpp) cc_final: 0.7207 (tpp) REVERT: A 295 VAL cc_start: 0.9077 (m) cc_final: 0.8866 (t) REVERT: A 305 LYS cc_start: 0.8160 (mtpp) cc_final: 0.7936 (mtpp) REVERT: A 312 LEU cc_start: 0.8471 (tp) cc_final: 0.8104 (tp) REVERT: B 100 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8615 (mp) REVERT: C 40 LYS cc_start: 0.7835 (ttmm) cc_final: 0.7419 (mtpp) REVERT: C 78 TYR cc_start: 0.8400 (p90) cc_final: 0.7924 (p90) REVERT: C 91 TYR cc_start: 0.8510 (t80) cc_final: 0.8287 (t80) REVERT: C 145 TYR cc_start: 0.8505 (m-80) cc_final: 0.8076 (m-80) REVERT: C 149 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8363 (tp) REVERT: C 165 TYR cc_start: 0.8342 (t80) cc_final: 0.8119 (t80) REVERT: C 207 TYR cc_start: 0.8425 (t80) cc_final: 0.8121 (t80) REVERT: C 219 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8233 (mtpp) REVERT: C 258 LYS cc_start: 0.7452 (ptpp) cc_final: 0.7167 (ptpp) REVERT: D 106 ARG cc_start: 0.8302 (tpm170) cc_final: 0.8065 (tpm170) outliers start: 20 outliers final: 10 residues processed: 309 average time/residue: 0.0857 time to fit residues: 36.2790 Evaluate side-chains 307 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 294 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 176 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 92 optimal weight: 0.0770 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 196 ASN C 74 ASN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107408 restraints weight = 12933.931| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.79 r_work: 0.3209 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8388 Z= 0.145 Angle : 0.562 12.716 11385 Z= 0.276 Chirality : 0.041 0.162 1248 Planarity : 0.004 0.044 1455 Dihedral : 3.925 17.101 1101 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.51 % Allowed : 19.50 % Favored : 78.00 % 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: -0.35 (0.26), residues: 1020 helix: 2.22 (0.37), residues: 216 sheet: 1.13 (0.35), residues: 225 loop : -1.92 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 106 TYR 0.021 0.001 TYR C 306 PHE 0.016 0.002 PHE C 111 TRP 0.011 0.001 TRP C 231 HIS 0.004 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8376) covalent geometry : angle 0.55645 (11361) SS BOND : bond 0.00213 ( 12) SS BOND : angle 1.78085 ( 24) hydrogen bonds : bond 0.03728 ( 248) hydrogen bonds : angle 4.49613 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 312 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 ILE cc_start: 0.8532 (tp) cc_final: 0.8180 (tp) REVERT: E 100 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7475 (mm-30) REVERT: E 133 THR cc_start: 0.8634 (m) cc_final: 0.8343 (t) REVERT: E 161 LEU cc_start: 0.8811 (tp) cc_final: 0.8598 (tt) REVERT: E 196 ASN cc_start: 0.8589 (t0) cc_final: 0.8309 (t0) REVERT: E 205 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8278 (mtmm) REVERT: E 266 MET cc_start: 0.7644 (tpp) cc_final: 0.7245 (tpp) REVERT: F 100 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8645 (mp) REVERT: A 40 LYS cc_start: 0.8332 (mtpp) cc_final: 0.8019 (mtpp) REVERT: A 57 VAL cc_start: 0.7725 (t) cc_final: 0.7345 (p) REVERT: A 61 ILE cc_start: 0.8462 (tp) cc_final: 0.8188 (tp) REVERT: A 142 ASN cc_start: 0.8462 (m-40) cc_final: 0.8235 (m-40) REVERT: A 213 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7637 (mt-10) REVERT: A 223 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7613 (mm-40) REVERT: A 227 MET cc_start: 0.8181 (ptp) cc_final: 0.7928 (ptp) REVERT: A 247 ASN cc_start: 0.7341 (m110) cc_final: 0.7120 (m110) REVERT: A 266 MET cc_start: 0.7785 (tpp) cc_final: 0.7326 (tpp) REVERT: A 295 VAL cc_start: 0.8998 (m) cc_final: 0.8691 (t) REVERT: A 305 LYS cc_start: 0.8281 (mtpp) cc_final: 0.8012 (mtpp) REVERT: A 312 LEU cc_start: 0.8493 (tp) cc_final: 0.8080 (tp) REVERT: B 100 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8621 (mp) REVERT: C 66 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8691 (mmtt) REVERT: C 78 TYR cc_start: 0.8399 (p90) cc_final: 0.7930 (p90) REVERT: C 91 TYR cc_start: 0.8520 (t80) cc_final: 0.8254 (t80) REVERT: C 145 TYR cc_start: 0.8504 (m-80) cc_final: 0.8083 (m-80) REVERT: C 149 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8360 (tp) REVERT: C 165 TYR cc_start: 0.8329 (t80) cc_final: 0.8112 (t80) REVERT: C 207 TYR cc_start: 0.8409 (t80) cc_final: 0.8161 (t80) REVERT: C 219 LYS cc_start: 0.8470 (mtpp) cc_final: 0.8233 (mtpp) REVERT: C 258 LYS cc_start: 0.7540 (ptpp) cc_final: 0.7235 (ptpp) outliers start: 23 outliers final: 13 residues processed: 317 average time/residue: 0.0826 time to fit residues: 36.0609 Evaluate side-chains 319 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 303 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain D residue 69 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 9 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 193 GLN A 167 ASN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106566 restraints weight = 13220.940| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.84 r_work: 0.3201 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8388 Z= 0.144 Angle : 0.550 10.343 11385 Z= 0.271 Chirality : 0.041 0.134 1248 Planarity : 0.004 0.035 1455 Dihedral : 3.861 15.935 1101 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.94 % Allowed : 21.46 % Favored : 75.60 % 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: -0.27 (0.26), residues: 1020 helix: 2.34 (0.37), residues: 216 sheet: 1.18 (0.35), residues: 225 loop : -1.89 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 106 TYR 0.017 0.001 TYR C 306 PHE 0.015 0.002 PHE C 111 TRP 0.008 0.001 TRP C 231 HIS 0.003 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8376) covalent geometry : angle 0.54543 (11361) SS BOND : bond 0.00231 ( 12) SS BOND : angle 1.63432 ( 24) hydrogen bonds : bond 0.03606 ( 248) hydrogen bonds : angle 4.39658 ( 705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 306 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 41 LEU cc_start: 0.7981 (mt) cc_final: 0.7747 (mt) REVERT: E 47 LYS cc_start: 0.7683 (mttt) cc_final: 0.7417 (mttt) REVERT: E 61 ILE cc_start: 0.8533 (tp) cc_final: 0.8167 (tp) REVERT: E 100 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7498 (mm-30) REVERT: E 103 GLU cc_start: 0.8096 (tp30) cc_final: 0.7634 (tp30) REVERT: E 196 ASN cc_start: 0.8616 (t0) cc_final: 0.8324 (t0) REVERT: E 205 LYS cc_start: 0.8514 (mtmm) cc_final: 0.8292 (mtmm) REVERT: E 258 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7326 (tptt) REVERT: E 266 MET cc_start: 0.7648 (tpp) cc_final: 0.7250 (tpp) REVERT: E 305 LYS cc_start: 0.8694 (tppp) cc_final: 0.8401 (tppp) REVERT: F 100 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8588 (mp) REVERT: A 40 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7927 (mtpp) REVERT: A 57 VAL cc_start: 0.7692 (t) cc_final: 0.7323 (p) REVERT: A 61 ILE cc_start: 0.8440 (tp) cc_final: 0.8131 (tp) REVERT: A 142 ASN cc_start: 0.8490 (m-40) cc_final: 0.8284 (m-40) REVERT: A 149 LEU cc_start: 0.8761 (tp) cc_final: 0.8447 (tt) REVERT: A 213 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7636 (mt-10) REVERT: A 223 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7650 (mm-40) REVERT: A 247 ASN cc_start: 0.7261 (m110) cc_final: 0.6970 (m110) REVERT: A 266 MET cc_start: 0.7767 (tpp) cc_final: 0.7333 (tpp) REVERT: A 295 VAL cc_start: 0.9026 (m) cc_final: 0.8731 (t) REVERT: A 305 LYS cc_start: 0.8455 (mtpp) cc_final: 0.8214 (mtpp) REVERT: A 312 LEU cc_start: 0.8534 (tp) cc_final: 0.8132 (tp) REVERT: B 100 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8629 (mp) REVERT: C 78 TYR cc_start: 0.8441 (p90) cc_final: 0.8010 (p90) REVERT: C 91 TYR cc_start: 0.8517 (t80) cc_final: 0.8232 (t80) REVERT: C 145 TYR cc_start: 0.8496 (m-80) cc_final: 0.8065 (m-80) REVERT: C 149 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8361 (tp) REVERT: C 207 TYR cc_start: 0.8417 (t80) cc_final: 0.8204 (t80) REVERT: C 219 LYS cc_start: 0.8475 (mtpp) cc_final: 0.8240 (mtpp) outliers start: 27 outliers final: 15 residues processed: 314 average time/residue: 0.0809 time to fit residues: 35.1549 Evaluate side-chains 320 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 301 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 258 LYS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 308 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 72 optimal weight: 0.0050 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 193 GLN A 167 ASN A 280 GLN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.107117 restraints weight = 13130.192| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.83 r_work: 0.3228 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8388 Z= 0.096 Angle : 0.525 9.084 11385 Z= 0.254 Chirality : 0.040 0.135 1248 Planarity : 0.004 0.038 1455 Dihedral : 3.747 16.901 1101 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.70 % Allowed : 22.44 % Favored : 73.86 % 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: -0.10 (0.26), residues: 1020 helix: 2.44 (0.37), residues: 216 sheet: 1.39 (0.35), residues: 222 loop : -1.79 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 106 TYR 0.014 0.001 TYR C 306 PHE 0.017 0.001 PHE E 292 TRP 0.008 0.001 TRP B 92 HIS 0.002 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8376) covalent geometry : angle 0.52176 (11361) SS BOND : bond 0.00183 ( 12) SS BOND : angle 1.44272 ( 24) hydrogen bonds : bond 0.03214 ( 248) hydrogen bonds : angle 4.39635 ( 705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 299 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 38 ASN cc_start: 0.8610 (p0) cc_final: 0.8368 (p0) REVERT: E 41 LEU cc_start: 0.8003 (mt) cc_final: 0.7757 (mt) REVERT: E 61 ILE cc_start: 0.8475 (tp) cc_final: 0.8086 (tp) REVERT: E 100 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7554 (mm-30) REVERT: E 103 GLU cc_start: 0.8089 (tp30) cc_final: 0.7531 (tp30) REVERT: E 196 ASN cc_start: 0.8601 (t0) cc_final: 0.8303 (t0) REVERT: E 205 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8271 (mtmm) REVERT: E 231 TRP cc_start: 0.8427 (p-90) cc_final: 0.7889 (p-90) REVERT: E 258 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7214 (mptt) REVERT: E 266 MET cc_start: 0.7671 (tpp) cc_final: 0.7250 (tpp) REVERT: E 305 LYS cc_start: 0.8689 (tppp) cc_final: 0.8342 (tppp) REVERT: F 100 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8580 (mp) REVERT: A 40 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7883 (mtpp) REVERT: A 57 VAL cc_start: 0.7632 (t) cc_final: 0.7257 (p) REVERT: A 61 ILE cc_start: 0.8445 (tp) cc_final: 0.8123 (tp) REVERT: A 142 ASN cc_start: 0.8471 (m-40) cc_final: 0.8252 (m-40) REVERT: A 149 LEU cc_start: 0.8774 (tp) cc_final: 0.8455 (tt) REVERT: A 213 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7623 (mt-10) REVERT: A 223 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7515 (mm-40) REVERT: A 247 ASN cc_start: 0.7110 (m110) cc_final: 0.6885 (m110) REVERT: A 266 MET cc_start: 0.7720 (tpp) cc_final: 0.7283 (tpp) REVERT: A 295 VAL cc_start: 0.8994 (m) cc_final: 0.8689 (t) REVERT: A 305 LYS cc_start: 0.8478 (mtpp) cc_final: 0.8254 (mmmm) REVERT: A 312 LEU cc_start: 0.8567 (tp) cc_final: 0.8160 (tp) REVERT: B 100 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8666 (mp) REVERT: C 40 LYS cc_start: 0.7775 (ttmm) cc_final: 0.7403 (mtpp) REVERT: C 78 TYR cc_start: 0.8426 (p90) cc_final: 0.8019 (p90) REVERT: C 91 TYR cc_start: 0.8486 (t80) cc_final: 0.8182 (t80) REVERT: C 145 TYR cc_start: 0.8465 (m-80) cc_final: 0.8031 (m-80) REVERT: C 149 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8368 (tp) REVERT: C 196 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8334 (t0) REVERT: C 207 TYR cc_start: 0.8395 (t80) cc_final: 0.8135 (t80) REVERT: C 208 LYS cc_start: 0.7727 (mtpp) cc_final: 0.7459 (mtpp) REVERT: C 219 LYS cc_start: 0.8449 (mtpp) cc_final: 0.8209 (mtpp) outliers start: 34 outliers final: 19 residues processed: 307 average time/residue: 0.0814 time to fit residues: 34.5670 Evaluate side-chains 316 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 292 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 258 LYS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 308 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 0.0670 chunk 60 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 193 GLN A 167 ASN A 280 GLN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.119091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106329 restraints weight = 12990.537| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.79 r_work: 0.3208 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8388 Z= 0.148 Angle : 0.544 8.909 11385 Z= 0.269 Chirality : 0.040 0.148 1248 Planarity : 0.004 0.038 1455 Dihedral : 3.794 17.128 1101 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.81 % Allowed : 22.98 % Favored : 73.20 % 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: -0.18 (0.26), residues: 1020 helix: 2.39 (0.37), residues: 216 sheet: 1.32 (0.36), residues: 225 loop : -1.85 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 113 TYR 0.016 0.001 TYR C 206 PHE 0.017 0.002 PHE E 292 TRP 0.008 0.001 TRP B 92 HIS 0.003 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8376) covalent geometry : angle 0.54057 (11361) SS BOND : bond 0.00231 ( 12) SS BOND : angle 1.39576 ( 24) hydrogen bonds : bond 0.03427 ( 248) hydrogen bonds : angle 4.33006 ( 705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 297 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 41 LEU cc_start: 0.8074 (mt) cc_final: 0.7838 (mt) REVERT: E 61 ILE cc_start: 0.8482 (tp) cc_final: 0.8094 (tp) REVERT: E 100 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7546 (mm-30) REVERT: E 103 GLU cc_start: 0.8075 (tp30) cc_final: 0.7492 (tp30) REVERT: E 112 GLU cc_start: 0.7639 (tt0) cc_final: 0.7423 (tp30) REVERT: E 196 ASN cc_start: 0.8604 (t0) cc_final: 0.8311 (t0) REVERT: E 205 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8278 (mtmm) REVERT: E 258 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7094 (mptt) REVERT: E 266 MET cc_start: 0.7650 (tpp) cc_final: 0.7280 (tpp) REVERT: E 305 LYS cc_start: 0.8737 (tppp) cc_final: 0.8345 (tppp) REVERT: F 100 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8593 (mp) REVERT: A 40 LYS cc_start: 0.8370 (mtpp) cc_final: 0.8073 (mtpp) REVERT: A 57 VAL cc_start: 0.7646 (t) cc_final: 0.7295 (p) REVERT: A 61 ILE cc_start: 0.8448 (tp) cc_final: 0.8147 (tp) REVERT: A 142 ASN cc_start: 0.8490 (m-40) cc_final: 0.8265 (m-40) REVERT: A 149 LEU cc_start: 0.8790 (tp) cc_final: 0.8467 (tt) REVERT: A 213 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7610 (mt-10) REVERT: A 223 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7563 (mm-40) REVERT: A 247 ASN cc_start: 0.7350 (m110) cc_final: 0.7061 (m110) REVERT: A 266 MET cc_start: 0.7712 (tpp) cc_final: 0.7284 (tpp) REVERT: A 295 VAL cc_start: 0.9061 (m) cc_final: 0.8785 (t) REVERT: A 305 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8356 (mmmm) REVERT: A 312 LEU cc_start: 0.8557 (tp) cc_final: 0.8152 (tp) REVERT: B 100 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8633 (mp) REVERT: C 78 TYR cc_start: 0.8362 (p90) cc_final: 0.7875 (p90) REVERT: C 91 TYR cc_start: 0.8474 (t80) cc_final: 0.7940 (t80) REVERT: C 145 TYR cc_start: 0.8497 (m-80) cc_final: 0.8037 (m-80) REVERT: C 149 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8345 (tp) REVERT: C 188 GLN cc_start: 0.8616 (mm110) cc_final: 0.8361 (tp40) REVERT: C 219 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8233 (mtpp) REVERT: C 227 MET cc_start: 0.8347 (ptp) cc_final: 0.7628 (ptp) outliers start: 35 outliers final: 25 residues processed: 308 average time/residue: 0.0815 time to fit residues: 34.8097 Evaluate side-chains 323 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 294 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 258 LYS Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain D residue 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN A 167 ASN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.104296 restraints weight = 13130.889| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.82 r_work: 0.3177 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8388 Z= 0.199 Angle : 0.577 9.173 11385 Z= 0.287 Chirality : 0.042 0.143 1248 Planarity : 0.004 0.038 1455 Dihedral : 3.953 17.144 1101 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.36 % Allowed : 23.09 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.26), residues: 1020 helix: 2.30 (0.37), residues: 216 sheet: 1.21 (0.36), residues: 225 loop : -1.94 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 209 TYR 0.018 0.001 TYR C 306 PHE 0.020 0.002 PHE E 292 TRP 0.011 0.001 TRP C 60 HIS 0.005 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8376) covalent geometry : angle 0.57369 (11361) SS BOND : bond 0.00263 ( 12) SS BOND : angle 1.52306 ( 24) hydrogen bonds : bond 0.03797 ( 248) hydrogen bonds : angle 4.35217 ( 705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 298 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 ILE cc_start: 0.8522 (tp) cc_final: 0.8292 (tp) REVERT: E 100 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7533 (mm-30) REVERT: E 103 GLU cc_start: 0.8078 (tp30) cc_final: 0.7463 (tp30) REVERT: E 112 GLU cc_start: 0.7620 (tt0) cc_final: 0.7399 (tp30) REVERT: E 196 ASN cc_start: 0.8643 (t0) cc_final: 0.8349 (t0) REVERT: E 258 LYS cc_start: 0.7565 (tptt) cc_final: 0.7118 (mptt) REVERT: E 266 MET cc_start: 0.7574 (tpp) cc_final: 0.7284 (tpp) REVERT: E 305 LYS cc_start: 0.8769 (tppp) cc_final: 0.8384 (tppp) REVERT: F 100 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8597 (mp) REVERT: A 57 VAL cc_start: 0.7674 (t) cc_final: 0.7322 (p) REVERT: A 61 ILE cc_start: 0.8448 (tp) cc_final: 0.8141 (tp) REVERT: A 142 ASN cc_start: 0.8531 (m-40) cc_final: 0.8331 (m-40) REVERT: A 149 LEU cc_start: 0.8808 (tp) cc_final: 0.8489 (tt) REVERT: A 196 ASN cc_start: 0.8840 (t0) cc_final: 0.8555 (t0) REVERT: A 213 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7562 (mt-10) REVERT: A 223 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7723 (mm-40) REVERT: A 234 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7377 (mt) REVERT: A 247 ASN cc_start: 0.7619 (m110) cc_final: 0.7410 (m110) REVERT: A 266 MET cc_start: 0.7755 (tpp) cc_final: 0.7331 (tpp) REVERT: A 295 VAL cc_start: 0.9064 (m) cc_final: 0.8773 (t) REVERT: A 305 LYS cc_start: 0.8611 (mtpp) cc_final: 0.8331 (mmmm) REVERT: A 312 LEU cc_start: 0.8501 (tp) cc_final: 0.8074 (tp) REVERT: B 100 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8627 (mp) REVERT: C 78 TYR cc_start: 0.8413 (p90) cc_final: 0.7967 (p90) REVERT: C 91 TYR cc_start: 0.8467 (t80) cc_final: 0.8029 (t80) REVERT: C 145 TYR cc_start: 0.8547 (m-80) cc_final: 0.8065 (m-80) REVERT: C 188 GLN cc_start: 0.8653 (mm110) cc_final: 0.8335 (tp40) REVERT: C 196 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8470 (t0) REVERT: C 219 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8259 (mtpp) REVERT: C 233 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7723 (mp) outliers start: 40 outliers final: 26 residues processed: 314 average time/residue: 0.0816 time to fit residues: 35.3611 Evaluate side-chains 328 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 297 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain D residue 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 ASN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.117295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.104595 restraints weight = 12986.993| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.77 r_work: 0.3171 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8388 Z= 0.234 Angle : 0.610 9.379 11385 Z= 0.306 Chirality : 0.043 0.217 1248 Planarity : 0.004 0.038 1455 Dihedral : 4.104 20.004 1101 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.92 % Allowed : 24.62 % Favored : 71.46 % 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: -0.43 (0.26), residues: 1020 helix: 2.18 (0.37), residues: 216 sheet: 1.15 (0.36), residues: 225 loop : -2.01 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 209 TYR 0.018 0.002 TYR C 306 PHE 0.023 0.002 PHE C 111 TRP 0.012 0.002 TRP A 60 HIS 0.006 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 8376) covalent geometry : angle 0.60596 (11361) SS BOND : bond 0.00255 ( 12) SS BOND : angle 1.60033 ( 24) hydrogen bonds : bond 0.03971 ( 248) hydrogen bonds : angle 4.36279 ( 705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 313 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 ILE cc_start: 0.8561 (tp) cc_final: 0.8337 (tp) REVERT: E 100 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7492 (mm-30) REVERT: E 196 ASN cc_start: 0.8689 (t0) cc_final: 0.8393 (t0) REVERT: E 258 LYS cc_start: 0.7673 (tptt) cc_final: 0.7241 (mptt) REVERT: E 266 MET cc_start: 0.7535 (tpp) cc_final: 0.7300 (tpp) REVERT: E 305 LYS cc_start: 0.8779 (tppp) cc_final: 0.8364 (tppp) REVERT: F 100 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8623 (mp) REVERT: A 57 VAL cc_start: 0.7697 (t) cc_final: 0.7332 (p) REVERT: A 61 ILE cc_start: 0.8441 (tp) cc_final: 0.8131 (tp) REVERT: A 149 LEU cc_start: 0.8781 (tp) cc_final: 0.8471 (tt) REVERT: A 196 ASN cc_start: 0.8870 (t0) cc_final: 0.8575 (t0) REVERT: A 208 LYS cc_start: 0.7904 (mtpp) cc_final: 0.7665 (ttmm) REVERT: A 213 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7557 (mt-10) REVERT: A 223 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7724 (mm-40) REVERT: A 266 MET cc_start: 0.7805 (tpp) cc_final: 0.7357 (tpp) REVERT: A 295 VAL cc_start: 0.9074 (m) cc_final: 0.8797 (t) REVERT: A 305 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8188 (mmmm) REVERT: A 312 LEU cc_start: 0.8460 (tp) cc_final: 0.8019 (tp) REVERT: B 100 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8617 (mp) REVERT: C 78 TYR cc_start: 0.8412 (p90) cc_final: 0.7897 (p90) REVERT: C 91 TYR cc_start: 0.8468 (t80) cc_final: 0.8194 (t80) REVERT: C 145 TYR cc_start: 0.8557 (m-80) cc_final: 0.8029 (m-80) REVERT: C 188 GLN cc_start: 0.8759 (mm110) cc_final: 0.8385 (tp40) REVERT: C 196 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8507 (t0) REVERT: C 219 LYS cc_start: 0.8516 (mtpp) cc_final: 0.8282 (mtpp) REVERT: C 233 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7720 (mp) outliers start: 36 outliers final: 29 residues processed: 326 average time/residue: 0.0814 time to fit residues: 36.8884 Evaluate side-chains 334 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 301 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain D residue 55 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 167 ASN A 280 GLN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.118609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106065 restraints weight = 12952.397| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.75 r_work: 0.3196 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8388 Z= 0.155 Angle : 0.608 13.217 11385 Z= 0.292 Chirality : 0.042 0.204 1248 Planarity : 0.004 0.039 1455 Dihedral : 4.054 20.572 1101 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.27 % Allowed : 25.16 % Favored : 71.57 % 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: -0.40 (0.26), residues: 1020 helix: 2.24 (0.37), residues: 216 sheet: 1.14 (0.36), residues: 225 loop : -1.99 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 113 TYR 0.015 0.001 TYR C 306 PHE 0.016 0.002 PHE C 111 TRP 0.010 0.001 TRP B 92 HIS 0.003 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8376) covalent geometry : angle 0.60498 (11361) SS BOND : bond 0.00216 ( 12) SS BOND : angle 1.48384 ( 24) hydrogen bonds : bond 0.03623 ( 248) hydrogen bonds : angle 4.39004 ( 705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 299 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 ILE cc_start: 0.8520 (tp) cc_final: 0.8115 (tp) REVERT: E 100 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7516 (mm-30) REVERT: E 103 GLU cc_start: 0.8036 (tp30) cc_final: 0.7376 (tp30) REVERT: E 196 ASN cc_start: 0.8660 (t0) cc_final: 0.8390 (t0) REVERT: E 258 LYS cc_start: 0.7543 (tptt) cc_final: 0.7081 (mptt) REVERT: E 305 LYS cc_start: 0.8805 (tppp) cc_final: 0.8363 (tppp) REVERT: F 100 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8604 (mp) REVERT: A 57 VAL cc_start: 0.7680 (t) cc_final: 0.7327 (p) REVERT: A 61 ILE cc_start: 0.8454 (tp) cc_final: 0.8147 (tp) REVERT: A 149 LEU cc_start: 0.8774 (tp) cc_final: 0.8422 (tt) REVERT: A 188 GLN cc_start: 0.8608 (tp40) cc_final: 0.8207 (tp40) REVERT: A 196 ASN cc_start: 0.8831 (t0) cc_final: 0.8504 (t0) REVERT: A 208 LYS cc_start: 0.7895 (mtpp) cc_final: 0.7643 (ttmm) REVERT: A 213 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7495 (mt-10) REVERT: A 223 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7642 (mm-40) REVERT: A 247 ASN cc_start: 0.7580 (m110) cc_final: 0.7273 (m110) REVERT: A 266 MET cc_start: 0.7816 (tpp) cc_final: 0.7369 (tpp) REVERT: A 295 VAL cc_start: 0.9058 (m) cc_final: 0.8760 (t) REVERT: A 305 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8164 (mmmm) REVERT: A 312 LEU cc_start: 0.8482 (tp) cc_final: 0.8050 (tp) REVERT: B 100 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8599 (mp) REVERT: C 40 LYS cc_start: 0.7795 (ttmm) cc_final: 0.7400 (mtpp) REVERT: C 78 TYR cc_start: 0.8417 (p90) cc_final: 0.7894 (p90) REVERT: C 91 TYR cc_start: 0.8464 (t80) cc_final: 0.8041 (t80) REVERT: C 145 TYR cc_start: 0.8522 (m-80) cc_final: 0.8001 (m-80) REVERT: C 172 GLU cc_start: 0.7737 (pt0) cc_final: 0.7401 (pt0) REVERT: C 219 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8252 (mtpp) REVERT: C 227 MET cc_start: 0.8407 (ptp) cc_final: 0.7823 (ptp) outliers start: 30 outliers final: 25 residues processed: 311 average time/residue: 0.0829 time to fit residues: 35.4561 Evaluate side-chains 328 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 301 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain D residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 0.0020 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 280 GLN ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.106652 restraints weight = 12935.483| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.78 r_work: 0.3212 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8388 Z= 0.135 Angle : 0.610 12.756 11385 Z= 0.291 Chirality : 0.042 0.207 1248 Planarity : 0.004 0.038 1455 Dihedral : 4.035 20.885 1101 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.16 % Allowed : 24.84 % Favored : 72.00 % 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: -0.38 (0.26), residues: 1020 helix: 2.24 (0.37), residues: 216 sheet: 1.16 (0.35), residues: 225 loop : -1.97 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 113 TYR 0.015 0.001 TYR C 306 PHE 0.015 0.001 PHE C 111 TRP 0.016 0.001 TRP A 252 HIS 0.003 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8376) covalent geometry : angle 0.60740 (11361) SS BOND : bond 0.00203 ( 12) SS BOND : angle 1.34833 ( 24) hydrogen bonds : bond 0.03481 ( 248) hydrogen bonds : angle 4.41023 ( 705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 300 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 ILE cc_start: 0.8495 (tp) cc_final: 0.8085 (tp) REVERT: E 100 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7486 (mm-30) REVERT: E 103 GLU cc_start: 0.8026 (tp30) cc_final: 0.7347 (tp30) REVERT: E 196 ASN cc_start: 0.8653 (t0) cc_final: 0.8382 (t0) REVERT: E 258 LYS cc_start: 0.7516 (tptt) cc_final: 0.7042 (mptt) REVERT: E 305 LYS cc_start: 0.8795 (tppp) cc_final: 0.8417 (tppp) REVERT: F 59 MET cc_start: 0.6943 (tpt) cc_final: 0.6571 (tpt) REVERT: F 100 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8591 (mp) REVERT: A 57 VAL cc_start: 0.7657 (t) cc_final: 0.7293 (p) REVERT: A 61 ILE cc_start: 0.8444 (tp) cc_final: 0.8123 (tp) REVERT: A 149 LEU cc_start: 0.8820 (tp) cc_final: 0.8463 (tt) REVERT: A 188 GLN cc_start: 0.8596 (tp40) cc_final: 0.8209 (tp40) REVERT: A 196 ASN cc_start: 0.8836 (t0) cc_final: 0.8521 (t0) REVERT: A 208 LYS cc_start: 0.7860 (mtpp) cc_final: 0.7609 (ttmm) REVERT: A 213 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7539 (mt-10) REVERT: A 223 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7577 (mm-40) REVERT: A 247 ASN cc_start: 0.7464 (m110) cc_final: 0.7175 (m110) REVERT: A 266 MET cc_start: 0.7838 (tpp) cc_final: 0.7361 (tpp) REVERT: A 295 VAL cc_start: 0.9075 (m) cc_final: 0.8798 (t) REVERT: A 305 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8156 (mmmm) REVERT: A 312 LEU cc_start: 0.8494 (tp) cc_final: 0.8053 (tp) REVERT: B 100 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8592 (mp) REVERT: C 78 TYR cc_start: 0.8421 (p90) cc_final: 0.7896 (p90) REVERT: C 91 TYR cc_start: 0.8456 (t80) cc_final: 0.8071 (t80) REVERT: C 145 TYR cc_start: 0.8509 (m-80) cc_final: 0.7978 (m-80) REVERT: C 172 GLU cc_start: 0.7789 (pt0) cc_final: 0.7460 (pt0) REVERT: C 196 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8481 (t0) REVERT: C 219 LYS cc_start: 0.8475 (mtpp) cc_final: 0.8230 (mtpp) REVERT: C 227 MET cc_start: 0.8418 (ptp) cc_final: 0.7805 (ptp) REVERT: C 286 LEU cc_start: 0.8817 (mt) cc_final: 0.8495 (mp) REVERT: D 69 GLU cc_start: 0.7448 (tp30) cc_final: 0.7241 (tp30) outliers start: 29 outliers final: 26 residues processed: 309 average time/residue: 0.0821 time to fit residues: 35.1403 Evaluate side-chains 326 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 297 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 259 LYS Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 135 SER Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 308 LYS Chi-restraints excluded: chain D residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 84 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 74 optimal weight: 0.4980 chunk 92 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.119050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.105920 restraints weight = 12986.130| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.85 r_work: 0.3202 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 8388 Z= 0.150 Angle : 1.178 59.188 11385 Z= 0.671 Chirality : 0.042 0.197 1248 Planarity : 0.004 0.039 1455 Dihedral : 4.093 20.736 1101 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.31 % Favored : 95.59 % Rotamer: Outliers : 3.16 % Allowed : 24.95 % Favored : 71.90 % Cbeta Deviations : 0.10 % 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: -0.37 (0.26), residues: 1020 helix: 2.25 (0.37), residues: 216 sheet: 1.17 (0.35), residues: 225 loop : -1.97 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 113 TYR 0.014 0.001 TYR C 306 PHE 0.015 0.002 PHE C 111 TRP 0.032 0.001 TRP A 252 HIS 0.003 0.001 HIS C 181 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8376) covalent geometry : angle 1.17633 (11361) SS BOND : bond 0.00200 ( 12) SS BOND : angle 1.68013 ( 24) hydrogen bonds : bond 0.03457 ( 248) hydrogen bonds : angle 4.43056 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1682.38 seconds wall clock time: 29 minutes 45.98 seconds (1785.98 seconds total)