Starting phenix.real_space_refine on Wed Feb 12 13:14:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wtz_21900/02_2025/6wtz_21900.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wtz_21900/02_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_21900/02_2025/6wtz_21900.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wtz_21900/02_2025/6wtz_21900.map" model { file = "/net/cci-nas-00/data/ceres_data/6wtz_21900/02_2025/6wtz_21900.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wtz_21900/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.33, 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: 1.80 Conformation dependent library (CDL) restraints added in 1.1 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: 0.80 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: 2.48 Time building geometry restraints manager: 2.10 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: 2.820 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 20.870 Find NCS groups from input model: 0.150 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- 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 : 0.836 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: 0.1816 time to fit residues: 72.3754 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 : 0.938 ------------------------------------------------------------------------------- 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 = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.154077 restraints weight = 9041.939| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.31 r_work: 0.3593 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.949 Fit side-chains REVERT: A 62 GLU cc_start: 0.8763 (tt0) cc_final: 0.8378 (tt0) REVERT: A 210 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7701 (ttmm) REVERT: B 50 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7517 (mm-40) REVERT: B 62 GLU cc_start: 0.8783 (tt0) cc_final: 0.8415 (tt0) REVERT: B 210 LYS cc_start: 0.8072 (ttpt) cc_final: 0.7471 (tppt) REVERT: B 219 LYS cc_start: 0.7525 (tttp) cc_final: 0.7142 (tttt) REVERT: B 272 SER cc_start: 0.7649 (m) cc_final: 0.7333 (t) REVERT: C 12 ASP cc_start: 0.7736 (p0) cc_final: 0.7407 (p0) REVERT: C 62 GLU cc_start: 0.8744 (tt0) cc_final: 0.8429 (tt0) REVERT: C 210 LYS cc_start: 0.7748 (ttpt) cc_final: 0.7472 (ttmm) REVERT: C 224 ASN cc_start: 0.8107 (m-40) cc_final: 0.7806 (m-40) REVERT: C 312 ASP cc_start: 0.8524 (t0) cc_final: 0.8306 (t0) REVERT: C 329 ASP cc_start: 0.6732 (m-30) cc_final: 0.6494 (m-30) outliers start: 23 outliers final: 16 residues processed: 227 average time/residue: 0.1769 time to fit residues: 55.4955 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 : 0.823 ------------------------------------------------------------------------------- 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: 0.8980 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 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 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 = 0.3775 r_free = 0.3775 target = 0.164081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.155298 restraints weight = 9113.772| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.27 r_work: 0.3607 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8049 Z= 0.302 Angle : 0.645 7.166 10890 Z= 0.360 Chirality : 0.046 0.141 1104 Planarity : 0.004 0.038 1470 Dihedral : 5.762 33.903 1141 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.93 % Allowed : 18.50 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.60 (0.26), residues: 1014 helix: -4.69 (0.18), residues: 18 sheet: 0.09 (0.22), residues: 588 loop : -2.69 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 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 234 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8762 (tt0) cc_final: 0.8429 (tt0) REVERT: A 71 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7987 (mt-10) REVERT: A 187 ILE cc_start: 0.7191 (tt) cc_final: 0.6950 (tt) REVERT: A 210 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7664 (ttmm) REVERT: B 62 GLU cc_start: 0.8769 (tt0) cc_final: 0.8443 (tt0) REVERT: B 157 TYR cc_start: 0.7523 (t80) cc_final: 0.6828 (t80) REVERT: B 210 LYS cc_start: 0.8081 (ttpt) cc_final: 0.7508 (tppt) REVERT: B 219 LYS cc_start: 0.7482 (tttp) cc_final: 0.7159 (tttt) REVERT: B 272 SER cc_start: 0.7777 (m) cc_final: 0.7468 (t) REVERT: C 12 ASP cc_start: 0.7651 (p0) cc_final: 0.7361 (p0) REVERT: C 62 GLU cc_start: 0.8779 (tt0) cc_final: 0.8487 (tt0) REVERT: C 210 LYS cc_start: 0.7754 (ttpt) cc_final: 0.7439 (ttmm) REVERT: C 329 ASP cc_start: 0.6633 (m-30) cc_final: 0.6415 (m-30) outliers start: 31 outliers final: 25 residues processed: 224 average time/residue: 0.1927 time to fit residues: 59.9163 Evaluate side-chains 217 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 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: 0.1980 chunk 3 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.164303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.155603 restraints weight = 9112.755| |-----------------------------------------------------------------------------| 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: 0.3516 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8049 Z= 0.280 Angle : 0.623 7.189 10890 Z= 0.348 Chirality : 0.046 0.140 1104 Planarity : 0.004 0.038 1470 Dihedral : 5.537 24.381 1140 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.44 % Allowed : 20.79 % Favored : 74.78 % 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: -1.51 (0.26), residues: 1014 helix: -4.32 (0.27), residues: 18 sheet: 0.05 (0.22), residues: 588 loop : -2.46 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 214 HIS 0.004 0.002 HIS C 21 PHE 0.022 0.002 PHE A 128 TYR 0.017 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 231 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8766 (tt0) cc_final: 0.8400 (tt0) REVERT: A 71 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7874 (mt-10) REVERT: A 187 ILE cc_start: 0.7159 (tt) cc_final: 0.6917 (tt) REVERT: A 210 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7585 (ttmm) REVERT: A 336 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8353 (tp) REVERT: B 62 GLU cc_start: 0.8779 (tt0) cc_final: 0.8459 (tt0) REVERT: B 157 TYR cc_start: 0.7564 (t80) cc_final: 0.7274 (t80) REVERT: B 210 LYS cc_start: 0.8097 (ttpt) cc_final: 0.7501 (tppt) REVERT: B 219 LYS cc_start: 0.7537 (tttp) cc_final: 0.7143 (tttt) REVERT: B 272 SER cc_start: 0.7698 (m) cc_final: 0.7370 (t) REVERT: C 12 ASP cc_start: 0.7546 (p0) cc_final: 0.7265 (p0) REVERT: C 62 GLU cc_start: 0.8787 (tt0) cc_final: 0.8505 (tt0) outliers start: 35 outliers final: 28 residues processed: 219 average time/residue: 0.1850 time to fit residues: 56.1720 Evaluate side-chains 224 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 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 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 330 ASP 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: 0.0870 chunk 87 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.164856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.156154 restraints weight = 9023.115| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.29 r_work: 0.3630 rms_B_bonded: 1.80 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: 0.7690 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8049 Z= 0.274 Angle : 0.617 7.165 10890 Z= 0.346 Chirality : 0.045 0.139 1104 Planarity : 0.004 0.038 1470 Dihedral : 5.469 24.039 1140 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.70 % Allowed : 20.53 % Favored : 73.76 % 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: -1.41 (0.25), residues: 1014 helix: -3.99 (0.37), residues: 18 sheet: 0.20 (0.22), residues: 567 loop : -2.43 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 214 HIS 0.004 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 B 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 235 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.871 Fit side-chains REVERT: A 62 GLU cc_start: 0.8768 (tt0) cc_final: 0.8404 (tt0) REVERT: A 187 ILE cc_start: 0.7158 (tt) cc_final: 0.6904 (tt) REVERT: A 210 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7598 (ttmm) REVERT: A 336 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8323 (tp) REVERT: B 30 ASN cc_start: 0.8158 (t0) cc_final: 0.7692 (t0) REVERT: B 62 GLU cc_start: 0.8761 (tt0) cc_final: 0.8459 (tt0) REVERT: B 157 TYR cc_start: 0.7574 (t80) cc_final: 0.7303 (t80) REVERT: B 210 LYS cc_start: 0.8085 (ttpt) cc_final: 0.7492 (tppt) REVERT: B 219 LYS cc_start: 0.7627 (tttp) cc_final: 0.7386 (ttmt) REVERT: B 272 SER cc_start: 0.7718 (m) cc_final: 0.7357 (t) REVERT: C 12 ASP cc_start: 0.7501 (p0) cc_final: 0.7239 (p0) REVERT: C 62 GLU cc_start: 0.8814 (tt0) cc_final: 0.8505 (tt0) REVERT: C 296 GLU cc_start: 0.7740 (tp30) cc_final: 0.7236 (tp30) REVERT: C 314 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.6869 (mm) outliers start: 45 outliers final: 35 residues processed: 222 average time/residue: 0.1744 time to fit residues: 53.7699 Evaluate side-chains 220 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.162118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.153890 restraints weight = 9063.645| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.20 r_work: 0.3592 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2842 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= 0.336 Angle : 0.661 7.247 10890 Z= 0.370 Chirality : 0.047 0.167 1104 Planarity : 0.004 0.037 1470 Dihedral : 5.628 25.109 1140 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 6.34 % Allowed : 20.79 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.68 (0.50), residues: 18 sheet: 0.17 (0.22), residues: 567 loop : -2.44 (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 A 21 PHE 0.021 0.002 PHE B 128 TYR 0.017 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 232 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8785 (tt0) cc_final: 0.8445 (tt0) REVERT: A 187 ILE cc_start: 0.7209 (tt) cc_final: 0.6935 (tt) REVERT: A 210 LYS cc_start: 0.8020 (ttpt) cc_final: 0.7584 (ttmm) REVERT: A 219 LYS cc_start: 0.7476 (tttp) cc_final: 0.7249 (tttt) REVERT: A 336 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8360 (tp) REVERT: B 13 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8356 (tp) REVERT: B 30 ASN cc_start: 0.8231 (t0) cc_final: 0.7792 (t0) REVERT: B 62 GLU cc_start: 0.8744 (tt0) cc_final: 0.8413 (tt0) REVERT: B 157 TYR cc_start: 0.7564 (t80) cc_final: 0.7251 (t80) REVERT: B 210 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7474 (tppt) REVERT: B 219 LYS cc_start: 0.7733 (tttp) cc_final: 0.7491 (ttmt) REVERT: C 38 MET cc_start: 0.8305 (mtp) cc_final: 0.8067 (ttm) REVERT: C 62 GLU cc_start: 0.8849 (tt0) cc_final: 0.8546 (tt0) REVERT: C 90 TYR cc_start: 0.7800 (t80) cc_final: 0.7418 (t80) REVERT: C 314 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6782 (mm) outliers start: 50 outliers final: 39 residues processed: 218 average time/residue: 0.1794 time to fit residues: 54.3637 Evaluate side-chains 222 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 311 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 51 ILE 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 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 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 314 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.162248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.153920 restraints weight = 9144.219| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.21 r_work: 0.3594 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2905 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= 0.328 Angle : 0.654 7.240 10890 Z= 0.366 Chirality : 0.046 0.141 1104 Planarity : 0.004 0.037 1470 Dihedral : 5.612 24.849 1140 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 6.46 % Allowed : 22.05 % Favored : 71.48 % 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: -1.39 (0.25), residues: 1014 helix: -3.51 (0.58), residues: 18 sheet: 0.23 (0.22), residues: 561 loop : -2.43 (0.24), residues: 435 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 229 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8781 (tt0) cc_final: 0.8449 (tt0) REVERT: A 187 ILE cc_start: 0.7204 (tt) cc_final: 0.6949 (tt) REVERT: A 210 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7558 (ttmm) REVERT: A 336 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8381 (tp) REVERT: B 13 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8348 (tp) REVERT: B 29 GLU cc_start: 0.7760 (pm20) cc_final: 0.7491 (pm20) REVERT: B 30 ASN cc_start: 0.8235 (t0) cc_final: 0.7806 (t0) REVERT: B 62 GLU cc_start: 0.8741 (tt0) cc_final: 0.8410 (tt0) REVERT: B 157 TYR cc_start: 0.7564 (t80) cc_final: 0.7231 (t80) REVERT: B 210 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7476 (tppt) REVERT: B 219 LYS cc_start: 0.7736 (tttp) cc_final: 0.7482 (ttmt) REVERT: C 38 MET cc_start: 0.8334 (mtp) cc_final: 0.8113 (ttm) REVERT: C 62 GLU cc_start: 0.8847 (tt0) cc_final: 0.8551 (tt0) REVERT: C 90 TYR cc_start: 0.7817 (t80) cc_final: 0.7420 (t80) REVERT: C 115 LEU cc_start: 0.8611 (mp) cc_final: 0.8405 (mp) outliers start: 51 outliers final: 42 residues processed: 214 average time/residue: 0.1776 time to fit residues: 52.9866 Evaluate side-chains 220 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 311 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 13 LEU 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 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 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 289 VAL Chi-restraints excluded: chain C residue 296 GLU 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: 0.6980 chunk 98 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 94 optimal weight: 0.0870 chunk 31 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.166631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.157796 restraints weight = 9052.057| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.29 r_work: 0.3646 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8049 Z= 0.224 Angle : 0.599 7.054 10890 Z= 0.336 Chirality : 0.045 0.148 1104 Planarity : 0.003 0.039 1470 Dihedral : 5.281 21.916 1140 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 6.21 % Allowed : 22.69 % 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 (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: -1.34 (0.25), residues: 1014 helix: -3.39 (0.59), residues: 18 sheet: 0.18 (0.22), residues: 567 loop : -2.31 (0.25), residues: 429 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 0.022 0.002 PHE A 128 TYR 0.015 0.001 TYR A 310 ARG 0.001 0.000 ARG A 196 *********************** 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 241 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8776 (tt0) cc_final: 0.8426 (tt0) REVERT: A 187 ILE cc_start: 0.7115 (tt) cc_final: 0.6864 (tt) REVERT: A 210 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7573 (ttmm) REVERT: A 336 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8260 (tp) REVERT: B 13 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8428 (tp) REVERT: B 29 GLU cc_start: 0.7728 (pm20) cc_final: 0.7482 (pm20) REVERT: B 30 ASN cc_start: 0.8170 (t0) cc_final: 0.7748 (t0) REVERT: B 62 GLU cc_start: 0.8768 (tt0) cc_final: 0.8460 (tt0) REVERT: B 157 TYR cc_start: 0.7552 (t80) cc_final: 0.7240 (t80) REVERT: B 210 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7533 (tppt) REVERT: B 219 LYS cc_start: 0.7636 (tttp) cc_final: 0.7400 (ttmt) REVERT: B 272 SER cc_start: 0.7666 (m) cc_final: 0.7288 (t) REVERT: C 62 GLU cc_start: 0.8821 (tt0) cc_final: 0.8531 (tt0) REVERT: C 90 TYR cc_start: 0.7755 (t80) cc_final: 0.7352 (t80) REVERT: C 115 LEU cc_start: 0.8555 (mp) cc_final: 0.8348 (mp) outliers start: 49 outliers final: 42 residues processed: 227 average time/residue: 0.1770 time to fit residues: 55.8582 Evaluate side-chains 229 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 336 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 13 LEU 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 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 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 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: 1.9990 chunk 72 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 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 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 = 0.3765 r_free = 0.3765 target = 0.163160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.154790 restraints weight = 9211.796| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.22 r_work: 0.3605 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2943 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 : 0.639 7.194 10890 Z= 0.358 Chirality : 0.046 0.141 1104 Planarity : 0.004 0.037 1470 Dihedral : 5.499 24.583 1140 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.70 % Allowed : 23.32 % Favored : 70.98 % 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: -3.14 (0.65), residues: 18 sheet: 0.22 (0.22), residues: 561 loop : -2.34 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 214 HIS 0.003 0.001 HIS C 21 PHE 0.021 0.002 PHE B 128 TYR 0.016 0.002 TYR A 310 ARG 0.002 0.000 ARG A 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 233 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8783 (tt0) cc_final: 0.8455 (tt0) REVERT: A 187 ILE cc_start: 0.7154 (tt) cc_final: 0.6895 (tt) REVERT: A 210 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7592 (ttmm) REVERT: B 13 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8441 (tp) REVERT: B 29 GLU cc_start: 0.7786 (pm20) cc_final: 0.7529 (pm20) REVERT: B 30 ASN cc_start: 0.8201 (t0) cc_final: 0.7798 (t0) REVERT: B 62 GLU cc_start: 0.8748 (tt0) cc_final: 0.8411 (tt0) REVERT: B 157 TYR cc_start: 0.7579 (t80) cc_final: 0.7232 (t80) REVERT: B 210 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7477 (tppt) REVERT: B 219 LYS cc_start: 0.7759 (tttp) cc_final: 0.7511 (ttmt) REVERT: C 38 MET cc_start: 0.8335 (mtp) cc_final: 0.8108 (ttm) REVERT: C 62 GLU cc_start: 0.8852 (tt0) cc_final: 0.8556 (tt0) REVERT: C 90 TYR cc_start: 0.7801 (t80) cc_final: 0.7422 (t80) REVERT: C 115 LEU cc_start: 0.8609 (mp) cc_final: 0.8400 (mp) REVERT: C 182 TYR cc_start: 0.8175 (t80) cc_final: 0.7865 (t80) outliers start: 45 outliers final: 41 residues processed: 221 average time/residue: 0.1759 time to fit residues: 54.5037 Evaluate side-chains 228 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 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 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 13 LEU 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 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 328 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 13 LEU 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: 0.2980 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 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** C 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.162565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.154298 restraints weight = 9054.657| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.20 r_work: 0.3600 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8049 Z= 0.336 Angle : 0.667 7.190 10890 Z= 0.373 Chirality : 0.047 0.209 1104 Planarity : 0.004 0.037 1470 Dihedral : 5.612 24.806 1140 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 6.21 % Allowed : 22.94 % Favored : 70.85 % 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: -1.32 (0.25), residues: 1014 helix: -3.04 (0.67), residues: 18 sheet: 0.29 (0.22), residues: 561 loop : -2.44 (0.24), residues: 435 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 0.017 0.002 TYR A 182 ARG 0.002 0.000 ARG A 82 ********************** 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 229 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8778 (tt0) cc_final: 0.8451 (tt0) REVERT: A 187 ILE cc_start: 0.7173 (tt) cc_final: 0.6914 (tt) REVERT: A 210 LYS cc_start: 0.8086 (ttpt) cc_final: 0.7607 (ttmm) REVERT: B 13 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8432 (tp) REVERT: B 29 GLU cc_start: 0.7767 (pm20) cc_final: 0.7533 (pm20) REVERT: B 30 ASN cc_start: 0.8227 (t0) cc_final: 0.7851 (t0) REVERT: B 62 GLU cc_start: 0.8731 (tt0) cc_final: 0.8403 (tt0) REVERT: B 210 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7477 (tppt) REVERT: B 219 LYS cc_start: 0.7766 (tttp) cc_final: 0.7343 (tttt) REVERT: C 38 MET cc_start: 0.8339 (mtp) cc_final: 0.8111 (ttm) REVERT: C 62 GLU cc_start: 0.8857 (tt0) cc_final: 0.8568 (tt0) REVERT: C 90 TYR cc_start: 0.7824 (t80) cc_final: 0.7429 (t80) REVERT: C 115 LEU cc_start: 0.8610 (mp) cc_final: 0.8400 (mp) REVERT: C 182 TYR cc_start: 0.8148 (t80) cc_final: 0.7854 (t80) outliers start: 49 outliers final: 43 residues processed: 216 average time/residue: 0.1864 time to fit residues: 56.2491 Evaluate side-chains 227 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 13 LEU 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 216 THR 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 328 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 13 LEU 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: 0.9990 chunk 94 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 79 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 chunk 11 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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** B 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 = 0.3817 r_free = 0.3817 target = 0.167458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.158523 restraints weight = 9108.341| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.31 r_work: 0.3655 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2964 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= 0.208 Angle : 0.598 7.036 10890 Z= 0.335 Chirality : 0.045 0.177 1104 Planarity : 0.003 0.038 1470 Dihedral : 5.211 21.398 1140 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.32 % Allowed : 23.70 % Favored : 70.98 % 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: -1.23 (0.25), residues: 1014 helix: -3.09 (0.60), residues: 18 sheet: 0.27 (0.22), residues: 561 loop : -2.25 (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 0.018 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: 3739.86 seconds wall clock time: 67 minutes 24.54 seconds (4044.54 seconds total)