Starting phenix.real_space_refine on Wed Mar 12 13:44:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wtz_21900/03_2025/6wtz_21900.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wtz_21900/03_2025/6wtz_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6wtz_21900/03_2025/6wtz_21900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wtz_21900/03_2025/6wtz_21900.map" model { file = "/net/cci-nas-00/data/ceres_data/6wtz_21900/03_2025/6wtz_21900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wtz_21900/03_2025/6wtz_21900.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.085 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: C, B 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: 5.28, per 1000 atoms: 0.67 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: 1.79 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.92 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: 2.17 Time building geometry restraints manager: 2.14 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.980 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.460 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.780 ------------------------------------------------------------------------------- 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= 0.266 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (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 TRP 0.013 0.003 TRP C 214 HIS 0.003 0.002 HIS B 21 PHE 0.027 0.003 PHE C 128 TYR 0.016 0.002 TYR A 310 ARG 0.002 0.000 ARG A 196 *********************** 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 : 0.790 Fit side-chains REVERT: A 25 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6986 (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: 0.6991 (OUTLIER) cc_final: 0.6754 (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: 0.7401 (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 219 LYS cc_start: 0.7387 (tttp) cc_final: 0.7071 (tttt) REVERT: B 279 LYS cc_start: 0.7354 (ttpt) cc_final: 0.7144 (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: 0.7593 (t0) REVERT: B 329 ASP cc_start: 0.6396 (m-30) cc_final: 0.6184 (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: 0.1690 time to fit residues: 67.8254 Evaluate side-chains 229 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 86 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 230 ASN A 262 GLN B 170 ASN B 262 GLN C 21 HIS C 170 ASN C 230 ASN C 236 ASN C 262 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.163222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.154137 restraints weight = 9041.934| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.30 r_work: 0.3590 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8049 Z= 0.413 Angle : 0.731 7.142 10890 Z= 0.405 Chirality : 0.049 0.147 1104 Planarity : 0.005 0.036 1470 Dihedral : 6.638 35.839 1184 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.92 % Allowed : 13.81 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.26), residues: 1014 helix: -4.96 (0.16), residues: 18 sheet: 0.15 (0.23), residues: 555 loop : -2.91 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 214 HIS 0.004 0.002 HIS C 21 PHE 0.027 0.003 PHE B 153 TYR 0.021 0.002 TYR A 310 ARG 0.004 0.001 ARG A 82 *********************** 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 235 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.876 Fit side-chains REVERT: A 62 GLU cc_start: 0.8769 (tt0) cc_final: 0.8387 (tt0) REVERT: A 210 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7720 (ttmm) REVERT: B 50 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7523 (mm-40) REVERT: B 62 GLU cc_start: 0.8793 (tt0) cc_final: 0.8430 (tt0) REVERT: B 210 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7486 (tppt) REVERT: B 219 LYS cc_start: 0.7543 (tttp) cc_final: 0.7164 (tttt) REVERT: B 272 SER cc_start: 0.7655 (m) cc_final: 0.7342 (t) REVERT: C 12 ASP cc_start: 0.7761 (p0) cc_final: 0.7435 (p0) REVERT: C 62 GLU cc_start: 0.8755 (tt0) cc_final: 0.8441 (tt0) REVERT: C 210 LYS cc_start: 0.7752 (ttpt) cc_final: 0.7486 (ttmm) REVERT: C 224 ASN cc_start: 0.8108 (m-40) cc_final: 0.7808 (m-40) REVERT: C 312 ASP cc_start: 0.8528 (t0) cc_final: 0.8314 (t0) REVERT: C 329 ASP cc_start: 0.6743 (m-30) cc_final: 0.6510 (m-30) outliers start: 23 outliers final: 16 residues processed: 227 average time/residue: 0.1771 time to fit residues: 55.5914 Evaluate side-chains 217 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 328 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 51 ILE 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 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 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 82 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 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 = 0.3791 r_free = 0.3791 target = 0.165411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.156544 restraints weight = 9154.615| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.27 r_work: 0.3627 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8049 Z= 0.262 Angle : 0.622 7.215 10890 Z= 0.347 Chirality : 0.046 0.143 1104 Planarity : 0.004 0.038 1470 Dihedral : 5.628 32.648 1141 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.68 % Allowed : 18.25 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.26), residues: 1014 helix: -4.72 (0.18), residues: 18 sheet: 0.11 (0.22), residues: 588 loop : -2.66 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 214 HIS 0.005 0.002 HIS C 21 PHE 0.023 0.002 PHE B 153 TYR 0.019 0.002 TYR A 310 ARG 0.003 0.000 ARG B 100 *********************** 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 231 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8759 (tt0) cc_final: 0.8417 (tt0) REVERT: A 71 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7948 (mt-10) REVERT: A 187 ILE cc_start: 0.7148 (tt) cc_final: 0.6910 (tt) REVERT: A 210 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7554 (ttmm) REVERT: B 62 GLU cc_start: 0.8733 (tt0) cc_final: 0.8397 (tt0) REVERT: B 157 TYR cc_start: 0.7495 (t80) cc_final: 0.7281 (t80) REVERT: B 210 LYS cc_start: 0.8080 (ttpt) cc_final: 0.7499 (tppt) REVERT: B 219 LYS cc_start: 0.7432 (tttp) cc_final: 0.7119 (tttt) REVERT: B 272 SER cc_start: 0.7743 (m) cc_final: 0.7455 (t) REVERT: C 12 ASP cc_start: 0.7560 (p0) cc_final: 0.7273 (p0) REVERT: C 62 GLU cc_start: 0.8772 (tt0) cc_final: 0.8461 (tt0) REVERT: C 210 LYS cc_start: 0.7755 (ttpt) cc_final: 0.7433 (ttmm) outliers start: 29 outliers final: 24 residues processed: 221 average time/residue: 0.1744 time to fit residues: 53.6443 Evaluate side-chains 212 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 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 187 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 311 VAL 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 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 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 37 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 61 optimal weight: 0.0570 chunk 94 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.8104 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.163631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.154975 restraints weight = 9108.540| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.28 r_work: 0.3615 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8049 Z= 0.319 Angle : 0.645 7.228 10890 Z= 0.361 Chirality : 0.046 0.140 1104 Planarity : 0.004 0.038 1470 Dihedral : 5.654 25.116 1140 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.56 % Allowed : 20.91 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.25), residues: 1014 helix: -4.37 (0.26), residues: 18 sheet: 0.18 (0.22), residues: 567 loop : -2.51 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 214 HIS 0.004 0.002 HIS C 21 PHE 0.022 0.002 PHE B 153 TYR 0.018 0.002 TYR A 310 ARG 0.002 0.000 ARG B 100 *********************** 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 227 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8764 (tt0) cc_final: 0.8403 (tt0) REVERT: A 187 ILE cc_start: 0.7183 (tt) cc_final: 0.6938 (tt) REVERT: A 210 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7656 (ttmm) REVERT: A 336 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8364 (tp) REVERT: B 62 GLU cc_start: 0.8768 (tt0) cc_final: 0.8457 (tt0) REVERT: B 157 TYR cc_start: 0.7567 (t80) cc_final: 0.7284 (t80) REVERT: B 210 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7537 (tppt) REVERT: B 219 LYS cc_start: 0.7593 (tttp) cc_final: 0.7179 (tttt) REVERT: B 272 SER cc_start: 0.7741 (m) cc_final: 0.7388 (t) REVERT: C 12 ASP cc_start: 0.7572 (p0) cc_final: 0.7291 (p0) REVERT: C 62 GLU cc_start: 0.8820 (tt0) cc_final: 0.8511 (tt0) outliers start: 36 outliers final: 27 residues processed: 215 average time/residue: 0.1730 time to fit residues: 51.7141 Evaluate side-chains 216 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 178 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 337 VAL 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 187 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 248 SER 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.163589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.154901 restraints weight = 9031.471| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.29 r_work: 0.3614 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2806 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= 0.314 Angle : 0.642 7.209 10890 Z= 0.359 Chirality : 0.046 0.140 1104 Planarity : 0.004 0.038 1470 Dihedral : 5.605 24.963 1140 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.70 % Allowed : 20.41 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.25), residues: 1014 helix: -3.97 (0.40), residues: 18 sheet: 0.19 (0.22), residues: 567 loop : -2.47 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 214 HIS 0.004 0.002 HIS C 21 PHE 0.021 0.002 PHE A 128 TYR 0.017 0.002 TYR A 310 ARG 0.002 0.000 ARG A 82 *********************** 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 233 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 0.856 Fit side-chains REVERT: A 62 GLU cc_start: 0.8768 (tt0) cc_final: 0.8411 (tt0) REVERT: A 187 ILE cc_start: 0.7179 (tt) cc_final: 0.6930 (tt) REVERT: A 210 LYS cc_start: 0.8046 (ttpt) cc_final: 0.7565 (ttmm) REVERT: A 336 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8357 (tp) REVERT: B 30 ASN cc_start: 0.8197 (t0) cc_final: 0.7765 (t0) REVERT: B 62 GLU cc_start: 0.8764 (tt0) cc_final: 0.8457 (tt0) REVERT: B 157 TYR cc_start: 0.7682 (t80) cc_final: 0.7364 (t80) REVERT: B 210 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7531 (tppt) REVERT: B 219 LYS cc_start: 0.7682 (tttp) cc_final: 0.7417 (ttmt) REVERT: B 272 SER cc_start: 0.7758 (m) cc_final: 0.7390 (t) REVERT: C 12 ASP cc_start: 0.7537 (p0) cc_final: 0.7274 (p0) REVERT: C 29 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: C 62 GLU cc_start: 0.8814 (tt0) cc_final: 0.8511 (tt0) REVERT: C 90 TYR cc_start: 0.7728 (t80) cc_final: 0.7327 (t80) REVERT: C 296 GLU cc_start: 0.7764 (tp30) cc_final: 0.7254 (tp30) REVERT: C 314 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6879 (mm) outliers start: 45 outliers final: 36 residues processed: 219 average time/residue: 0.1768 time to fit residues: 53.8620 Evaluate side-chains 222 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 152 ASN Chi-restraints excluded: chain A residue 178 ILE 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 336 ILE Chi-restraints excluded: chain A residue 337 VAL 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 187 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 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 314 ILE 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 15 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 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 30 ASN ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.163675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.154997 restraints weight = 9109.651| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.28 r_work: 0.3619 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8049 Z= 0.301 Angle : 0.637 7.214 10890 Z= 0.357 Chirality : 0.046 0.163 1104 Planarity : 0.004 0.038 1470 Dihedral : 5.552 24.846 1140 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.25), residues: 1014 helix: -3.72 (0.50), residues: 18 sheet: 0.18 (0.22), residues: 567 loop : -2.42 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 214 HIS 0.003 0.001 HIS C 21 PHE 0.022 0.002 PHE A 128 TYR 0.016 0.002 TYR A 310 ARG 0.002 0.000 ARG A 82 *********************** 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 238 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 0.814 Fit side-chains REVERT: A 62 GLU cc_start: 0.8775 (tt0) cc_final: 0.8428 (tt0) REVERT: A 187 ILE cc_start: 0.7156 (tt) cc_final: 0.6908 (tt) REVERT: A 210 LYS cc_start: 0.7954 (ttpt) cc_final: 0.7501 (ttmm) REVERT: A 336 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8347 (tp) REVERT: B 30 ASN cc_start: 0.8241 (t0) cc_final: 0.7811 (t0) REVERT: B 62 GLU cc_start: 0.8761 (tt0) cc_final: 0.8428 (tt0) REVERT: B 157 TYR cc_start: 0.7566 (t80) cc_final: 0.7270 (t80) REVERT: B 210 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7533 (tppt) REVERT: B 219 LYS cc_start: 0.7687 (tttp) cc_final: 0.7451 (ttmt) REVERT: B 272 SER cc_start: 0.7603 (m) cc_final: 0.7179 (t) REVERT: B 296 GLU cc_start: 0.7825 (tp30) cc_final: 0.7436 (tp30) REVERT: B 312 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7942 (t0) REVERT: C 29 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: C 38 MET cc_start: 0.8279 (mtp) cc_final: 0.8045 (ttm) REVERT: C 62 GLU cc_start: 0.8829 (tt0) cc_final: 0.8519 (tt0) REVERT: C 90 TYR cc_start: 0.7735 (t80) cc_final: 0.7360 (t80) REVERT: C 314 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6785 (mm) outliers start: 51 outliers final: 38 residues processed: 225 average time/residue: 0.1648 time to fit residues: 51.9750 Evaluate side-chains 226 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 152 ASN Chi-restraints excluded: chain A residue 178 ILE 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 336 ILE 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 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 187 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 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 314 ILE Chi-restraints excluded: chain C residue 330 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 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.162109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.153818 restraints weight = 9135.791| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.21 r_work: 0.3592 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8049 Z= 0.334 Angle : 0.654 7.233 10890 Z= 0.366 Chirality : 0.046 0.141 1104 Planarity : 0.004 0.037 1470 Dihedral : 5.628 24.942 1140 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 6.46 % Allowed : 21.93 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.25), residues: 1014 helix: -3.47 (0.60), residues: 18 sheet: 0.14 (0.22), residues: 567 loop : -2.41 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 214 HIS 0.003 0.001 HIS C 21 PHE 0.021 0.002 PHE A 128 TYR 0.016 0.002 TYR A 310 ARG 0.002 0.000 ARG A 82 *********************** 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 231 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 180 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8781 (tt0) cc_final: 0.8445 (tt0) REVERT: A 187 ILE cc_start: 0.7178 (tt) cc_final: 0.6912 (tt) REVERT: A 210 LYS cc_start: 0.7938 (ttpt) cc_final: 0.7506 (ttmm) REVERT: A 330 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7144 (m-30) REVERT: A 336 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8409 (tp) REVERT: B 29 GLU cc_start: 0.7748 (pm20) cc_final: 0.7491 (pm20) REVERT: B 62 GLU cc_start: 0.8738 (tt0) cc_final: 0.8415 (tt0) REVERT: B 157 TYR cc_start: 0.7567 (t80) cc_final: 0.7235 (t80) REVERT: B 210 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7468 (tppt) REVERT: B 219 LYS cc_start: 0.7736 (tttp) cc_final: 0.7487 (ttmt) REVERT: B 296 GLU cc_start: 0.7832 (tp30) cc_final: 0.7524 (tp30) REVERT: B 312 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7946 (t0) REVERT: C 38 MET cc_start: 0.8321 (mtp) cc_final: 0.8094 (ttm) REVERT: C 62 GLU cc_start: 0.8847 (tt0) cc_final: 0.8550 (tt0) REVERT: C 90 TYR cc_start: 0.7754 (t80) cc_final: 0.7343 (t80) REVERT: C 115 LEU cc_start: 0.8613 (mp) cc_final: 0.8404 (mp) outliers start: 51 outliers final: 42 residues processed: 217 average time/residue: 0.1661 time to fit residues: 50.5174 Evaluate side-chains 225 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 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 330 ASP Chi-restraints excluded: chain A residue 336 ILE 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 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 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 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 248 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 330 ASP 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 86 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.164956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.156165 restraints weight = 9081.099| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.29 r_work: 0.3632 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8049 Z= 0.262 Angle : 0.615 7.124 10890 Z= 0.345 Chirality : 0.045 0.146 1104 Planarity : 0.003 0.038 1470 Dihedral : 5.417 23.320 1140 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 6.21 % Allowed : 23.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1014 helix: -3.45 (0.59), residues: 18 sheet: 0.15 (0.22), residues: 567 loop : -2.34 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 214 HIS 0.003 0.001 HIS C 21 PHE 0.022 0.002 PHE A 128 TYR 0.015 0.002 TYR A 310 ARG 0.001 0.000 ARG B 82 *********************** 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 238 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 0.902 Fit side-chains REVERT: A 62 GLU cc_start: 0.8777 (tt0) cc_final: 0.8431 (tt0) REVERT: A 187 ILE cc_start: 0.7147 (tt) cc_final: 0.6905 (tt) REVERT: A 210 LYS cc_start: 0.7994 (ttpt) cc_final: 0.7518 (ttmm) REVERT: A 336 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8314 (tp) REVERT: B 30 ASN cc_start: 0.8198 (t0) cc_final: 0.7764 (t0) REVERT: B 62 GLU cc_start: 0.8770 (tt0) cc_final: 0.8469 (tt0) REVERT: B 157 TYR cc_start: 0.7534 (t80) cc_final: 0.7241 (t80) REVERT: B 210 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7506 (tppt) REVERT: B 219 LYS cc_start: 0.7665 (tttp) cc_final: 0.7424 (ttmt) REVERT: B 272 SER cc_start: 0.7597 (m) cc_final: 0.7169 (t) REVERT: B 296 GLU cc_start: 0.7770 (tp30) cc_final: 0.7455 (tp30) REVERT: B 312 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7805 (t0) REVERT: C 29 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: C 38 MET cc_start: 0.8300 (mtp) cc_final: 0.8074 (ttm) REVERT: C 62 GLU cc_start: 0.8819 (tt0) cc_final: 0.8509 (tt0) REVERT: C 90 TYR cc_start: 0.7793 (t80) cc_final: 0.7370 (t80) REVERT: C 115 LEU cc_start: 0.8579 (mp) cc_final: 0.8371 (mp) outliers start: 49 outliers final: 44 residues processed: 224 average time/residue: 0.1860 time to fit residues: 59.1705 Evaluate side-chains 236 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 256 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 336 ILE 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 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 289 VAL 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 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 209 LYS Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 336 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 5 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.163512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.155084 restraints weight = 9213.762| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.22 r_work: 0.3610 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8049 Z= 0.281 Angle : 0.628 7.179 10890 Z= 0.352 Chirality : 0.046 0.141 1104 Planarity : 0.004 0.038 1470 Dihedral : 5.464 24.061 1140 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 6.59 % Allowed : 22.94 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.25), residues: 1014 helix: -3.30 (0.64), residues: 18 sheet: 0.22 (0.22), residues: 561 loop : -2.33 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 214 HIS 0.003 0.001 HIS C 21 PHE 0.022 0.002 PHE A 128 TYR 0.015 0.002 TYR A 310 ARG 0.001 0.000 ARG B 82 *********************** 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 240 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 0.908 Fit side-chains REVERT: A 62 GLU cc_start: 0.8782 (tt0) cc_final: 0.8441 (tt0) REVERT: A 187 ILE cc_start: 0.7144 (tt) cc_final: 0.6897 (tt) REVERT: A 210 LYS cc_start: 0.7986 (ttpt) cc_final: 0.7585 (ttmm) REVERT: B 29 GLU cc_start: 0.7749 (pm20) cc_final: 0.7491 (pm20) REVERT: B 30 ASN cc_start: 0.8196 (t0) cc_final: 0.7796 (t0) REVERT: B 62 GLU cc_start: 0.8747 (tt0) cc_final: 0.8423 (tt0) REVERT: B 210 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7554 (tppt) REVERT: B 219 LYS cc_start: 0.7705 (tttp) cc_final: 0.7471 (ttmt) REVERT: B 296 GLU cc_start: 0.7750 (tp30) cc_final: 0.7480 (tp30) REVERT: B 312 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7863 (t0) REVERT: C 29 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: C 38 MET cc_start: 0.8354 (mtp) cc_final: 0.8133 (ttm) REVERT: C 62 GLU cc_start: 0.8840 (tt0) cc_final: 0.8543 (tt0) REVERT: C 90 TYR cc_start: 0.7825 (t80) cc_final: 0.7403 (t80) REVERT: C 115 LEU cc_start: 0.8599 (mp) cc_final: 0.8390 (mp) outliers start: 52 outliers final: 45 residues processed: 226 average time/residue: 0.1687 time to fit residues: 53.4883 Evaluate side-chains 233 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 104 VAL 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 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 88 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 187 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 289 VAL 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 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 209 LYS Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 336 ILE 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 95 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 27 optimal weight: 0.0030 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN C 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.167458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.158547 restraints weight = 9047.619| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.30 r_work: 0.3654 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8049 Z= 0.208 Angle : 0.590 7.024 10890 Z= 0.331 Chirality : 0.045 0.213 1104 Planarity : 0.003 0.038 1470 Dihedral : 5.191 21.763 1140 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.45 % Allowed : 23.95 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.25), residues: 1014 helix: -3.33 (0.59), residues: 18 sheet: 0.29 (0.22), residues: 561 loop : -2.31 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 214 HIS 0.003 0.001 HIS C 21 PHE 0.023 0.002 PHE C 128 TYR 0.017 0.001 TYR A 182 ARG 0.001 0.000 ARG A 196 ********************** 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 234 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.807 Fit side-chains REVERT: A 62 GLU cc_start: 0.8779 (tt0) cc_final: 0.8454 (tt0) REVERT: A 187 ILE cc_start: 0.7088 (tt) cc_final: 0.6843 (tt) REVERT: A 210 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7604 (ttmm) REVERT: B 29 GLU cc_start: 0.7758 (pm20) cc_final: 0.7527 (pm20) REVERT: B 30 ASN cc_start: 0.8186 (t0) cc_final: 0.7793 (t0) REVERT: B 62 GLU cc_start: 0.8803 (tt0) cc_final: 0.8498 (tt0) REVERT: B 210 LYS cc_start: 0.8086 (ttpt) cc_final: 0.7492 (tppt) REVERT: B 219 LYS cc_start: 0.7610 (tttp) cc_final: 0.7372 (ttmt) REVERT: B 272 SER cc_start: 0.7662 (m) cc_final: 0.7310 (t) REVERT: B 296 GLU cc_start: 0.7685 (tp30) cc_final: 0.7400 (tp30) REVERT: B 312 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7721 (t0) REVERT: C 29 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: C 38 MET cc_start: 0.8285 (mtp) cc_final: 0.8066 (ttm) REVERT: C 62 GLU cc_start: 0.8818 (tt0) cc_final: 0.8530 (tt0) REVERT: C 90 TYR cc_start: 0.7751 (t80) cc_final: 0.7338 (t80) REVERT: C 115 LEU cc_start: 0.8578 (mp) cc_final: 0.8377 (mp) REVERT: C 182 TYR cc_start: 0.8108 (t80) cc_final: 0.7729 (t80) outliers start: 43 outliers final: 38 residues processed: 221 average time/residue: 0.1774 time to fit residues: 54.7047 Evaluate side-chains 229 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 104 VAL 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 256 ASP 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 174 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 312 ASP 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 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 328 SER Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 336 ILE 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 36 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 79 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 11 optimal weight: 0.0040 chunk 89 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 overall best weight: 0.3730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.169165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.160398 restraints weight = 9040.700| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.27 r_work: 0.3678 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8049 Z= 0.183 Angle : 0.573 7.069 10890 Z= 0.322 Chirality : 0.044 0.168 1104 Planarity : 0.003 0.039 1470 Dihedral : 5.003 20.861 1140 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.20 % Allowed : 24.33 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.26), residues: 1014 helix: -2.97 (0.65), residues: 18 sheet: 0.31 (0.22), residues: 561 loop : -2.11 (0.26), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 214 HIS 0.003 0.001 HIS C 21 PHE 0.023 0.002 PHE A 128 TYR 0.019 0.001 TYR A 182 ARG 0.001 0.000 ARG A 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3790.43 seconds wall clock time: 66 minutes 0.82 seconds (3960.82 seconds total)