Starting phenix.real_space_refine on Tue Mar 3 18:21:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wtz_21900/03_2026/6wtz_21900.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wtz_21900/03_2026/6wtz_21900.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wtz_21900/03_2026/6wtz_21900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wtz_21900/03_2026/6wtz_21900.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wtz_21900/03_2026/6wtz_21900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wtz_21900/03_2026/6wtz_21900.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.085 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 9 5.16 5 C 4962 2.51 5 N 1314 2.21 5 O 1632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7917 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2627 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 335} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Restraints were copied for chains: B, C Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ASN A 27 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 27 " occ=0.00 residue: pdb=" N ASN B 27 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN B 27 " occ=0.00 residue: pdb=" N ASN C 27 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN C 27 " occ=0.00 Time building chain proxies: 1.75, per 1000 atoms: 0.22 Number of scatterers: 7917 At special positions: 0 Unit cell: (92.88, 95.04, 69.12, 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 9 16.00 O 1632 8.00 N 1314 7.00 C 4962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 301.5 milliseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1752 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 6 sheets defined 4.4% alpha, 45.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.523A pdb=" N ALA A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 110 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.524A pdb=" N ALA B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 110 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.524A pdb=" N ALA C 202 " --> pdb=" O ASN C 198 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2 through 5 current: chain 'A' and resid 56 through 66 removed outlier: 3.587A pdb=" N LEU A 83 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN A 64 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR A 81 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A 95 " --> pdb=" O TYR A 139 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR A 139 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP A 97 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA A 137 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY A 99 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA A 229 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 253 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA A 280 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASP A 290 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASP A 282 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASP A 288 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 297 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 15 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2 through 5 current: chain 'B' and resid 56 through 66 removed outlier: 3.587A pdb=" N LEU B 83 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 64 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR B 81 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER B 95 " --> pdb=" O TYR B 139 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR B 139 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP B 97 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA B 137 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLY B 99 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 229 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 253 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA B 280 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASP B 290 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 282 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASP B 288 " --> pdb=" O ASP B 282 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 297 " --> pdb=" O TYR B 313 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 15 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 242 Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 5 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 2 through 5 current: chain 'C' and resid 56 through 66 removed outlier: 3.587A pdb=" N LEU C 83 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN C 64 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N THR C 81 " --> pdb=" O ASN C 64 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER C 95 " --> pdb=" O TYR C 139 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR C 139 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP C 97 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA C 137 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLY C 99 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C 229 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS C 253 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA C 280 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASP C 290 " --> pdb=" O ALA C 280 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP C 282 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP C 288 " --> pdb=" O ASP C 282 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 297 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 15 " --> pdb=" O PHE C 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 239 through 242 354 hydrogen bonds defined for protein. 999 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: 1.29 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2631 1.34 - 1.45: 1534 1.45 - 1.57: 3866 1.57 - 1.68: 0 1.68 - 1.80: 18 Bond restraints: 8049 Sorted by residual: bond pdb=" N PHE B 144 " pdb=" CA PHE B 144 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.17e-02 7.31e+03 3.11e+00 bond pdb=" N PHE C 144 " pdb=" CA PHE C 144 " ideal model delta sigma weight residual 1.457 1.478 -0.020 1.17e-02 7.31e+03 3.00e+00 bond pdb=" N PHE A 144 " pdb=" CA PHE A 144 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.17e-02 7.31e+03 2.88e+00 bond pdb=" C LYS B 219 " pdb=" N TYR B 220 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.28e-02 6.10e+03 2.58e+00 bond pdb=" C LYS A 219 " pdb=" N TYR A 220 " ideal model delta sigma weight residual 1.330 1.350 -0.020 1.28e-02 6.10e+03 2.53e+00 ... (remaining 8044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 10373 1.73 - 3.45: 439 3.45 - 5.18: 56 5.18 - 6.90: 19 6.90 - 8.63: 3 Bond angle restraints: 10890 Sorted by residual: angle pdb=" C ASP A 127 " pdb=" N PHE A 128 " pdb=" CA PHE A 128 " ideal model delta sigma weight residual 121.54 130.17 -8.63 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C ASP C 127 " pdb=" N PHE C 128 " pdb=" CA PHE C 128 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" C ASP B 127 " pdb=" N PHE B 128 " pdb=" CA PHE B 128 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C ASN A 143 " pdb=" N PHE A 144 " pdb=" CA PHE A 144 " ideal model delta sigma weight residual 121.19 127.38 -6.19 1.59e+00 3.96e-01 1.51e+01 angle pdb=" C ASN C 143 " pdb=" N PHE C 144 " pdb=" CA PHE C 144 " ideal model delta sigma weight residual 121.19 127.33 -6.14 1.59e+00 3.96e-01 1.49e+01 ... (remaining 10885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4038 17.65 - 35.30: 390 35.30 - 52.95: 102 52.95 - 70.60: 27 70.60 - 88.25: 9 Dihedral angle restraints: 4566 sinusoidal: 1710 harmonic: 2856 Sorted by residual: dihedral pdb=" CA ASN A 143 " pdb=" C ASN A 143 " pdb=" N PHE A 144 " pdb=" CA PHE A 144 " ideal model delta harmonic sigma weight residual -180.00 -138.76 -41.24 0 5.00e+00 4.00e-02 6.80e+01 dihedral pdb=" CA ASN B 143 " pdb=" C ASN B 143 " pdb=" N PHE B 144 " pdb=" CA PHE B 144 " ideal model delta harmonic sigma weight residual 180.00 -138.81 -41.19 0 5.00e+00 4.00e-02 6.79e+01 dihedral pdb=" CA ASN C 143 " pdb=" C ASN C 143 " pdb=" N PHE C 144 " pdb=" CA PHE C 144 " ideal model delta harmonic sigma weight residual -180.00 -138.83 -41.17 0 5.00e+00 4.00e-02 6.78e+01 ... (remaining 4563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 828 0.052 - 0.105: 214 0.105 - 0.157: 55 0.157 - 0.209: 4 0.209 - 0.261: 3 Chirality restraints: 1104 Sorted by residual: chirality pdb=" CB ILE C 336 " pdb=" CA ILE C 336 " pdb=" CG1 ILE C 336 " pdb=" CG2 ILE C 336 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE A 336 " pdb=" CA ILE A 336 " pdb=" CG1 ILE A 336 " pdb=" CG2 ILE A 336 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE B 336 " pdb=" CA ILE B 336 " pdb=" CG1 ILE B 336 " pdb=" CG2 ILE B 336 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1101 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 115 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO B 116 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 116 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 116 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 115 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.47e+00 pdb=" N PRO C 116 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 116 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 116 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 115 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO A 116 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " 0.033 5.00e-02 4.00e+02 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2543 2.82 - 3.34: 6096 3.34 - 3.86: 13126 3.86 - 4.38: 15448 4.38 - 4.90: 28034 Nonbonded interactions: 65247 Sorted by model distance: nonbonded pdb=" OH TYR C 32 " pdb=" OD1 ASP C 121 " model vdw 2.301 3.040 nonbonded pdb=" OH TYR B 32 " pdb=" OD1 ASP B 121 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR A 32 " pdb=" OD1 ASP A 121 " model vdw 2.302 3.040 nonbonded pdb=" N ASP A 149 " pdb=" OD1 ASP A 149 " model vdw 2.307 3.120 nonbonded pdb=" N ASP B 149 " pdb=" OD1 ASP B 149 " model vdw 2.307 3.120 ... (remaining 65242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.020 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8049 Z= 0.211 Angle : 0.839 8.630 10890 Z= 0.496 Chirality : 0.052 0.261 1104 Planarity : 0.005 0.059 1470 Dihedral : 15.731 88.250 2814 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.70 % Allowed : 5.70 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.25), residues: 1014 helix: -5.21 (0.18), residues: 18 sheet: 0.12 (0.23), residues: 543 loop : -3.37 (0.22), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.016 0.002 TYR A 310 PHE 0.027 0.003 PHE C 128 TRP 0.013 0.003 TRP C 214 HIS 0.003 0.002 HIS B 21 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8049) covalent geometry : angle 0.83869 (10890) hydrogen bonds : bond 0.24140 ( 354) hydrogen bonds : angle 9.74578 ( 999) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 0.296 Fit side-chains REVERT: A 25 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6987 (ptpt) REVERT: A 62 GLU cc_start: 0.8445 (tt0) cc_final: 0.7943 (tt0) REVERT: A 66 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8191 (mm-40) REVERT: A 210 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.6976 (ttmm) REVERT: A 290 ASP cc_start: 0.7561 (m-30) cc_final: 0.6566 (p0) REVERT: A 312 ASP cc_start: 0.8235 (t0) cc_final: 0.7989 (t0) REVERT: A 329 ASP cc_start: 0.6308 (m-30) cc_final: 0.5931 (m-30) REVERT: B 10 LYS cc_start: 0.7840 (pttm) cc_final: 0.7209 (ptmt) REVERT: B 12 ASP cc_start: 0.6949 (p0) cc_final: 0.6717 (p0) REVERT: B 25 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6753 (mttm) REVERT: B 48 GLU cc_start: 0.7465 (tp30) cc_final: 0.7223 (tp30) REVERT: B 62 GLU cc_start: 0.8484 (tt0) cc_final: 0.7990 (tt0) REVERT: B 95 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8244 (p) REVERT: B 114 MET cc_start: 0.7615 (mmm) cc_final: 0.7402 (mmm) REVERT: B 187 ILE cc_start: 0.7098 (tt) cc_final: 0.6848 (tt) REVERT: B 210 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6861 (ttmm) REVERT: B 279 LYS cc_start: 0.7354 (ttpt) cc_final: 0.7143 (ttpt) REVERT: B 290 ASP cc_start: 0.7280 (m-30) cc_final: 0.6354 (p0) REVERT: B 312 ASP cc_start: 0.7987 (t0) cc_final: 0.7594 (t0) REVERT: B 329 ASP cc_start: 0.6395 (m-30) cc_final: 0.6185 (m-30) REVERT: B 339 GLN cc_start: 0.7676 (pt0) cc_final: 0.7456 (pt0) REVERT: C 62 GLU cc_start: 0.8235 (tt0) cc_final: 0.7777 (tt0) REVERT: C 210 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6902 (ttmm) REVERT: C 224 ASN cc_start: 0.7960 (m-40) cc_final: 0.7685 (m-40) REVERT: C 231 TYR cc_start: 0.7717 (t80) cc_final: 0.6991 (t80) REVERT: C 290 ASP cc_start: 0.7350 (m-30) cc_final: 0.6462 (p0) REVERT: C 329 ASP cc_start: 0.6866 (m-30) cc_final: 0.6420 (m-30) outliers start: 45 outliers final: 14 residues processed: 291 average time/residue: 0.0751 time to fit residues: 30.7005 Evaluate side-chains 228 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 328 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.0770 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS A 170 ASN A 262 GLN B 170 ASN B 262 GLN C 21 HIS C 170 ASN C 236 ASN C 262 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.166363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.157672 restraints weight = 8990.487| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.21 r_work: 0.3636 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8049 Z= 0.214 Angle : 0.668 7.155 10890 Z= 0.371 Chirality : 0.047 0.144 1104 Planarity : 0.004 0.037 1470 Dihedral : 6.309 32.898 1184 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.41 % Allowed : 14.07 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.26), residues: 1014 helix: -5.01 (0.16), residues: 18 sheet: 0.17 (0.23), residues: 558 loop : -2.86 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 100 TYR 0.020 0.002 TYR A 310 PHE 0.026 0.002 PHE A 153 TRP 0.014 0.002 TRP C 214 HIS 0.004 0.002 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 8049) covalent geometry : angle 0.66768 (10890) hydrogen bonds : bond 0.04643 ( 354) hydrogen bonds : angle 6.66671 ( 999) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8750 (tt0) cc_final: 0.8370 (tt0) REVERT: A 210 LYS cc_start: 0.8055 (ttpt) cc_final: 0.7546 (ttmm) REVERT: A 290 ASP cc_start: 0.7484 (m-30) cc_final: 0.6829 (p0) REVERT: A 296 GLU cc_start: 0.7816 (tp30) cc_final: 0.7596 (tp30) REVERT: B 50 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7555 (mm-40) REVERT: B 62 GLU cc_start: 0.8771 (tt0) cc_final: 0.8407 (tt0) REVERT: B 187 ILE cc_start: 0.7387 (tt) cc_final: 0.7167 (tt) REVERT: B 210 LYS cc_start: 0.8031 (ttpt) cc_final: 0.7465 (tppt) REVERT: B 272 SER cc_start: 0.7713 (m) cc_final: 0.7464 (t) REVERT: B 290 ASP cc_start: 0.7528 (m-30) cc_final: 0.6613 (p0) REVERT: C 12 ASP cc_start: 0.7606 (p0) cc_final: 0.7281 (p0) REVERT: C 38 MET cc_start: 0.8117 (mtp) cc_final: 0.7883 (mmm) REVERT: C 62 GLU cc_start: 0.8720 (tt0) cc_final: 0.8409 (tt0) REVERT: C 224 ASN cc_start: 0.8010 (m-40) cc_final: 0.7776 (m-40) outliers start: 19 outliers final: 13 residues processed: 220 average time/residue: 0.0715 time to fit residues: 22.4271 Evaluate side-chains 205 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 152 ASN B 152 ASN C 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.164888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.155908 restraints weight = 9090.830| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.30 r_work: 0.3612 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8049 Z= 0.206 Angle : 0.641 7.156 10890 Z= 0.358 Chirality : 0.046 0.146 1104 Planarity : 0.004 0.037 1470 Dihedral : 5.640 25.165 1141 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.42 % Allowed : 17.87 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.26), residues: 1014 helix: -4.79 (0.17), residues: 18 sheet: 0.14 (0.22), residues: 588 loop : -2.60 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 100 TYR 0.021 0.002 TYR A 310 PHE 0.022 0.002 PHE B 153 TRP 0.012 0.002 TRP C 214 HIS 0.004 0.002 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 8049) covalent geometry : angle 0.64140 (10890) hydrogen bonds : bond 0.04256 ( 354) hydrogen bonds : angle 6.41702 ( 999) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8771 (tt0) cc_final: 0.8424 (tt0) REVERT: A 187 ILE cc_start: 0.7162 (tt) cc_final: 0.6901 (tt) REVERT: A 210 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7700 (ttmm) REVERT: B 50 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7569 (mm-40) REVERT: B 62 GLU cc_start: 0.8743 (tt0) cc_final: 0.8414 (tt0) REVERT: B 157 TYR cc_start: 0.7503 (t80) cc_final: 0.6798 (t80) REVERT: B 187 ILE cc_start: 0.7428 (tt) cc_final: 0.7221 (tt) REVERT: B 210 LYS cc_start: 0.8039 (ttpt) cc_final: 0.7469 (tppt) REVERT: B 272 SER cc_start: 0.7763 (m) cc_final: 0.7439 (t) REVERT: C 12 ASP cc_start: 0.7645 (p0) cc_final: 0.7347 (p0) REVERT: C 62 GLU cc_start: 0.8752 (tt0) cc_final: 0.8456 (tt0) outliers start: 27 outliers final: 23 residues processed: 209 average time/residue: 0.0718 time to fit residues: 21.3551 Evaluate side-chains 211 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN C 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.164089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.155284 restraints weight = 9231.003| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.31 r_work: 0.3611 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8049 Z= 0.221 Angle : 0.646 7.150 10890 Z= 0.361 Chirality : 0.047 0.175 1104 Planarity : 0.004 0.037 1470 Dihedral : 5.635 24.473 1140 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 5.07 % Allowed : 20.03 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.26), residues: 1014 helix: -4.38 (0.25), residues: 18 sheet: 0.12 (0.22), residues: 588 loop : -2.52 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 100 TYR 0.020 0.002 TYR A 310 PHE 0.021 0.002 PHE A 128 TRP 0.012 0.003 TRP C 214 HIS 0.004 0.002 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 8049) covalent geometry : angle 0.64552 (10890) hydrogen bonds : bond 0.04126 ( 354) hydrogen bonds : angle 6.34133 ( 999) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8758 (tt0) cc_final: 0.8392 (tt0) REVERT: A 71 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7956 (mt-10) REVERT: A 187 ILE cc_start: 0.7184 (tt) cc_final: 0.6935 (tt) REVERT: A 210 LYS cc_start: 0.8147 (ttpt) cc_final: 0.7680 (ttmm) REVERT: B 62 GLU cc_start: 0.8715 (tt0) cc_final: 0.8393 (tt0) REVERT: B 157 TYR cc_start: 0.7560 (t80) cc_final: 0.7271 (t80) REVERT: B 187 ILE cc_start: 0.7469 (tt) cc_final: 0.7252 (tt) REVERT: B 210 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7529 (tppt) REVERT: B 272 SER cc_start: 0.7741 (m) cc_final: 0.7386 (t) REVERT: C 12 ASP cc_start: 0.7621 (p0) cc_final: 0.7322 (p0) REVERT: C 62 GLU cc_start: 0.8805 (tt0) cc_final: 0.8495 (tt0) outliers start: 40 outliers final: 30 residues processed: 209 average time/residue: 0.0710 time to fit residues: 21.1204 Evaluate side-chains 213 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 GLN C 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.163745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.154968 restraints weight = 9223.503| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.31 r_work: 0.3614 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8049 Z= 0.221 Angle : 0.646 7.219 10890 Z= 0.361 Chirality : 0.046 0.139 1104 Planarity : 0.004 0.036 1470 Dihedral : 5.626 25.031 1140 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 6.21 % Allowed : 19.65 % Favored : 74.14 % 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: -1.43 (0.25), residues: 1014 helix: -4.08 (0.37), residues: 18 sheet: 0.19 (0.22), residues: 567 loop : -2.46 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 100 TYR 0.018 0.002 TYR A 310 PHE 0.021 0.002 PHE A 128 TRP 0.012 0.003 TRP A 214 HIS 0.004 0.002 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 8049) covalent geometry : angle 0.64618 (10890) hydrogen bonds : bond 0.04062 ( 354) hydrogen bonds : angle 6.30357 ( 999) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8772 (tt0) cc_final: 0.8413 (tt0) REVERT: A 71 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7964 (mt-10) REVERT: A 187 ILE cc_start: 0.7188 (tt) cc_final: 0.6920 (tt) REVERT: A 210 LYS cc_start: 0.8103 (ttpt) cc_final: 0.7604 (ttmm) REVERT: B 30 ASN cc_start: 0.8188 (t0) cc_final: 0.7754 (t0) REVERT: B 62 GLU cc_start: 0.8742 (tt0) cc_final: 0.8429 (tt0) REVERT: B 157 TYR cc_start: 0.7633 (t80) cc_final: 0.7302 (t80) REVERT: B 187 ILE cc_start: 0.7486 (tt) cc_final: 0.7274 (tt) REVERT: B 210 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7524 (tppt) REVERT: B 272 SER cc_start: 0.7739 (m) cc_final: 0.7362 (t) REVERT: C 12 ASP cc_start: 0.7616 (p0) cc_final: 0.7321 (p0) REVERT: C 29 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7593 (pm20) REVERT: C 62 GLU cc_start: 0.8807 (tt0) cc_final: 0.8509 (tt0) REVERT: C 90 TYR cc_start: 0.7682 (t80) cc_final: 0.7303 (t80) outliers start: 49 outliers final: 39 residues processed: 222 average time/residue: 0.0714 time to fit residues: 22.7491 Evaluate side-chains 223 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 0.9980 chunk 100 optimal weight: 0.2980 chunk 48 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.164348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.155686 restraints weight = 9029.408| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.28 r_work: 0.3617 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8049 Z= 0.203 Angle : 0.630 7.189 10890 Z= 0.353 Chirality : 0.046 0.137 1104 Planarity : 0.004 0.037 1470 Dihedral : 5.525 24.925 1140 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 6.34 % Allowed : 20.66 % Favored : 73.00 % 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: -1.39 (0.25), residues: 1014 helix: -3.82 (0.44), residues: 18 sheet: 0.20 (0.22), residues: 567 loop : -2.40 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 82 TYR 0.017 0.002 TYR A 310 PHE 0.021 0.002 PHE A 128 TRP 0.012 0.003 TRP C 214 HIS 0.004 0.002 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 8049) covalent geometry : angle 0.62984 (10890) hydrogen bonds : bond 0.03896 ( 354) hydrogen bonds : angle 6.24989 ( 999) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 190 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8781 (tt0) cc_final: 0.8422 (tt0) REVERT: A 71 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7886 (mt-10) REVERT: A 187 ILE cc_start: 0.7204 (tt) cc_final: 0.6959 (tt) REVERT: A 210 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7618 (ttmm) REVERT: B 30 ASN cc_start: 0.8194 (t0) cc_final: 0.7754 (t0) REVERT: B 62 GLU cc_start: 0.8758 (tt0) cc_final: 0.8461 (tt0) REVERT: B 157 TYR cc_start: 0.7565 (t80) cc_final: 0.7266 (t80) REVERT: B 187 ILE cc_start: 0.7487 (tt) cc_final: 0.7271 (tt) REVERT: B 210 LYS cc_start: 0.8138 (ttpt) cc_final: 0.7544 (tppt) REVERT: B 272 SER cc_start: 0.7704 (m) cc_final: 0.7313 (t) REVERT: C 29 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: C 62 GLU cc_start: 0.8817 (tt0) cc_final: 0.8536 (tt0) REVERT: C 90 TYR cc_start: 0.7674 (t80) cc_final: 0.7345 (t80) outliers start: 50 outliers final: 37 residues processed: 225 average time/residue: 0.0711 time to fit residues: 23.0682 Evaluate side-chains 228 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 50 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.166164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.157288 restraints weight = 9139.374| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.31 r_work: 0.3642 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8049 Z= 0.167 Angle : 0.601 7.091 10890 Z= 0.338 Chirality : 0.045 0.189 1104 Planarity : 0.003 0.038 1470 Dihedral : 5.316 22.075 1140 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 6.46 % Allowed : 20.79 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.25), residues: 1014 helix: -3.67 (0.44), residues: 18 sheet: 0.22 (0.22), residues: 567 loop : -2.31 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 82 TYR 0.023 0.002 TYR B 182 PHE 0.022 0.002 PHE A 128 TRP 0.012 0.002 TRP C 214 HIS 0.004 0.001 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8049) covalent geometry : angle 0.60143 (10890) hydrogen bonds : bond 0.03657 ( 354) hydrogen bonds : angle 6.11203 ( 999) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 198 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8767 (tt0) cc_final: 0.8427 (tt0) REVERT: A 71 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7855 (mt-10) REVERT: A 187 ILE cc_start: 0.7146 (tt) cc_final: 0.6893 (tt) REVERT: A 210 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7632 (ttmm) REVERT: B 30 ASN cc_start: 0.8171 (t0) cc_final: 0.7742 (t0) REVERT: B 62 GLU cc_start: 0.8771 (tt0) cc_final: 0.8469 (tt0) REVERT: B 157 TYR cc_start: 0.7551 (t80) cc_final: 0.7242 (t80) REVERT: B 187 ILE cc_start: 0.7420 (tt) cc_final: 0.7161 (tt) REVERT: B 210 LYS cc_start: 0.8129 (ttpt) cc_final: 0.7561 (tppt) REVERT: B 272 SER cc_start: 0.7528 (m) cc_final: 0.7144 (t) REVERT: C 29 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7689 (pm20) REVERT: C 62 GLU cc_start: 0.8809 (tt0) cc_final: 0.8518 (tt0) REVERT: C 90 TYR cc_start: 0.7690 (t80) cc_final: 0.7335 (t80) REVERT: C 296 GLU cc_start: 0.7780 (tp30) cc_final: 0.7420 (tp30) REVERT: C 314 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6892 (mm) outliers start: 51 outliers final: 40 residues processed: 232 average time/residue: 0.0685 time to fit residues: 22.9346 Evaluate side-chains 237 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 26 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 95 optimal weight: 0.3980 chunk 48 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.168093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.159182 restraints weight = 9087.404| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.30 r_work: 0.3665 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8049 Z= 0.141 Angle : 0.582 7.045 10890 Z= 0.327 Chirality : 0.045 0.170 1104 Planarity : 0.003 0.039 1470 Dihedral : 5.123 20.758 1140 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.20 % Allowed : 22.94 % Favored : 71.86 % 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: -1.20 (0.26), residues: 1014 helix: -3.45 (0.46), residues: 18 sheet: 0.26 (0.22), residues: 567 loop : -2.19 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 196 TYR 0.015 0.001 TYR A 310 PHE 0.023 0.002 PHE B 128 TRP 0.012 0.002 TRP B 214 HIS 0.002 0.001 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8049) covalent geometry : angle 0.58184 (10890) hydrogen bonds : bond 0.03469 ( 354) hydrogen bonds : angle 6.02587 ( 999) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8770 (tt0) cc_final: 0.8431 (tt0) REVERT: A 187 ILE cc_start: 0.7086 (tt) cc_final: 0.6841 (tt) REVERT: A 210 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7622 (ttmm) REVERT: B 29 GLU cc_start: 0.7728 (pm20) cc_final: 0.7449 (pm20) REVERT: B 30 ASN cc_start: 0.8171 (t0) cc_final: 0.7737 (t0) REVERT: B 62 GLU cc_start: 0.8741 (tt0) cc_final: 0.8431 (tt0) REVERT: B 157 TYR cc_start: 0.7565 (t80) cc_final: 0.7272 (t80) REVERT: B 210 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7558 (tppt) REVERT: B 272 SER cc_start: 0.7607 (m) cc_final: 0.7267 (t) REVERT: C 29 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7682 (pm20) REVERT: C 62 GLU cc_start: 0.8816 (tt0) cc_final: 0.8524 (tt0) REVERT: C 90 TYR cc_start: 0.7678 (t80) cc_final: 0.7328 (t80) REVERT: C 314 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6871 (mm) outliers start: 41 outliers final: 33 residues processed: 221 average time/residue: 0.0711 time to fit residues: 22.5292 Evaluate side-chains 226 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.164151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.155353 restraints weight = 9074.415| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.29 r_work: 0.3622 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8049 Z= 0.219 Angle : 0.642 7.233 10890 Z= 0.360 Chirality : 0.046 0.155 1104 Planarity : 0.004 0.038 1470 Dihedral : 5.488 25.323 1140 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.96 % Allowed : 22.94 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.25), residues: 1014 helix: -3.18 (0.57), residues: 18 sheet: 0.26 (0.22), residues: 561 loop : -2.27 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 82 TYR 0.017 0.002 TYR A 310 PHE 0.021 0.002 PHE B 128 TRP 0.011 0.003 TRP A 214 HIS 0.003 0.002 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 8049) covalent geometry : angle 0.64156 (10890) hydrogen bonds : bond 0.03930 ( 354) hydrogen bonds : angle 6.24002 ( 999) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 0.284 Fit side-chains REVERT: A 62 GLU cc_start: 0.8770 (tt0) cc_final: 0.8422 (tt0) REVERT: A 187 ILE cc_start: 0.7174 (tt) cc_final: 0.6909 (tt) REVERT: A 210 LYS cc_start: 0.8071 (ttpt) cc_final: 0.7623 (ttmm) REVERT: A 219 LYS cc_start: 0.7513 (tttp) cc_final: 0.7303 (tttp) REVERT: B 29 GLU cc_start: 0.7767 (pm20) cc_final: 0.7525 (pm20) REVERT: B 30 ASN cc_start: 0.8186 (t0) cc_final: 0.7782 (t0) REVERT: B 62 GLU cc_start: 0.8765 (tt0) cc_final: 0.8430 (tt0) REVERT: B 210 LYS cc_start: 0.8098 (ttpt) cc_final: 0.7488 (ttmm) REVERT: C 29 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7611 (pm20) REVERT: C 38 MET cc_start: 0.8296 (mtp) cc_final: 0.8031 (ttm) REVERT: C 62 GLU cc_start: 0.8816 (tt0) cc_final: 0.8534 (tt0) REVERT: C 90 TYR cc_start: 0.7678 (t80) cc_final: 0.7306 (t80) outliers start: 47 outliers final: 38 residues processed: 217 average time/residue: 0.0716 time to fit residues: 22.1530 Evaluate side-chains 221 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 90 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 0.0070 chunk 42 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.166375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.157524 restraints weight = 9008.653| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.29 r_work: 0.3648 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8049 Z= 0.169 Angle : 0.606 7.053 10890 Z= 0.340 Chirality : 0.045 0.149 1104 Planarity : 0.003 0.037 1470 Dihedral : 5.278 22.210 1140 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.32 % Allowed : 23.45 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.25), residues: 1014 helix: -3.11 (0.55), residues: 18 sheet: 0.30 (0.22), residues: 561 loop : -2.23 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 82 TYR 0.027 0.002 TYR B 182 PHE 0.022 0.002 PHE B 128 TRP 0.012 0.002 TRP C 214 HIS 0.003 0.001 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8049) covalent geometry : angle 0.60612 (10890) hydrogen bonds : bond 0.03637 ( 354) hydrogen bonds : angle 6.10086 ( 999) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 0.254 Fit side-chains REVERT: A 62 GLU cc_start: 0.8772 (tt0) cc_final: 0.8445 (tt0) REVERT: A 187 ILE cc_start: 0.7121 (tt) cc_final: 0.6872 (tt) REVERT: A 210 LYS cc_start: 0.8069 (ttpt) cc_final: 0.7611 (ttmm) REVERT: A 219 LYS cc_start: 0.7346 (tttp) cc_final: 0.7131 (tttt) REVERT: B 29 GLU cc_start: 0.7756 (pm20) cc_final: 0.7502 (pm20) REVERT: B 30 ASN cc_start: 0.8144 (t0) cc_final: 0.7744 (t0) REVERT: B 62 GLU cc_start: 0.8781 (tt0) cc_final: 0.8472 (tt0) REVERT: B 210 LYS cc_start: 0.8101 (ttpt) cc_final: 0.7478 (ttmm) REVERT: B 272 SER cc_start: 0.7667 (m) cc_final: 0.7300 (t) REVERT: C 29 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: C 62 GLU cc_start: 0.8817 (tt0) cc_final: 0.8520 (tt0) REVERT: C 90 TYR cc_start: 0.7695 (t80) cc_final: 0.7336 (t80) REVERT: C 182 TYR cc_start: 0.8180 (t80) cc_final: 0.7874 (t80) outliers start: 42 outliers final: 40 residues processed: 218 average time/residue: 0.0740 time to fit residues: 23.1998 Evaluate side-chains 230 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN C 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.162791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.154326 restraints weight = 8967.969| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.23 r_work: 0.3597 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8049 Z= 0.230 Angle : 0.660 7.187 10890 Z= 0.369 Chirality : 0.047 0.154 1104 Planarity : 0.004 0.036 1470 Dihedral : 5.561 25.720 1140 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.96 % Allowed : 23.32 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.25), residues: 1014 helix: -2.95 (0.64), residues: 18 sheet: 0.26 (0.22), residues: 561 loop : -2.32 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 82 TYR 0.018 0.002 TYR A 182 PHE 0.021 0.002 PHE B 128 TRP 0.011 0.003 TRP A 214 HIS 0.003 0.002 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 8049) covalent geometry : angle 0.65981 (10890) hydrogen bonds : bond 0.03996 ( 354) hydrogen bonds : angle 6.28344 ( 999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1803.39 seconds wall clock time: 31 minutes 40.21 seconds (1900.21 seconds total)