Starting phenix.real_space_refine on Mon Mar 11 09:45:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtz_21900/03_2024/6wtz_21900.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtz_21900/03_2024/6wtz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtz_21900/03_2024/6wtz_21900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtz_21900/03_2024/6wtz_21900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtz_21900/03_2024/6wtz_21900.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wtz_21900/03_2024/6wtz_21900.pdb" } 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 Residue "A GLU 2": "OE1" <-> "OE2" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A ASP 113": "OD1" <-> "OD2" Residue "A ASP 149": "OD1" <-> "OD2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "B GLU 2": "OE1" <-> "OE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B ASP 113": "OD1" <-> "OD2" Residue "B ASP 149": "OD1" <-> "OD2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C ASP 107": "OD1" <-> "OD2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C ASP 149": "OD1" <-> "OD2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 164": "OD1" <-> "OD2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 319": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7917 Number of models: 1 Model: "" Number of chains: 6 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: "B" 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: "C" 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} 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: 4.64, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 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: 2.63 Conformation dependent library (CDL) restraints added in 1.4 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: 0.89 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: 2.45 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2631 1.34 - 1.45: 1534 1.45 - 1.57: 3866 1.57 - 1.68: 0 1.68 - 1.80: 18 Bond restraints: 8049 Sorted by residual: bond pdb=" N PHE B 144 " pdb=" CA PHE B 144 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.17e-02 7.31e+03 3.11e+00 bond pdb=" N PHE C 144 " pdb=" CA PHE C 144 " ideal model delta sigma weight residual 1.457 1.478 -0.020 1.17e-02 7.31e+03 3.00e+00 bond pdb=" N PHE A 144 " pdb=" CA PHE A 144 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.17e-02 7.31e+03 2.88e+00 bond pdb=" C LYS B 219 " pdb=" N TYR B 220 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.28e-02 6.10e+03 2.58e+00 bond pdb=" C LYS A 219 " pdb=" N TYR A 220 " ideal model delta sigma weight residual 1.330 1.350 -0.020 1.28e-02 6.10e+03 2.53e+00 ... (remaining 8044 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.18: 90 107.18 - 113.90: 4059 113.90 - 120.62: 3368 120.62 - 127.33: 3341 127.33 - 134.05: 32 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 2.440 nonbonded pdb=" OH TYR B 32 " pdb=" OD1 ASP B 121 " model vdw 2.302 2.440 nonbonded pdb=" OH TYR A 32 " pdb=" OD1 ASP A 121 " model vdw 2.302 2.440 nonbonded pdb=" N ASP A 149 " pdb=" OD1 ASP A 149 " model vdw 2.307 2.520 nonbonded pdb=" N ASP B 149 " pdb=" OD1 ASP B 149 " model vdw 2.307 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 8.800 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.360 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.490 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 45 poor density : 268 time to evaluate : 0.884 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: 0.1815 time to fit residues: 72.5109 Evaluate side-chains 229 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 209 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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: 0.7980 chunk 77 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS A 30 ASN A 170 ASN A 262 GLN B 170 ASN B 262 GLN C 21 HIS C 170 ASN C 236 ASN C 262 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2136 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= 0.308 Angle : 0.656 6.929 10890 Z= 0.363 Chirality : 0.046 0.144 1104 Planarity : 0.004 0.036 1470 Dihedral : 6.507 54.455 1184 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.30 % Allowed : 13.56 % Favored : 83.14 % 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: -1.71 (0.26), residues: 1014 helix: -5.01 (0.16), residues: 18 sheet: 0.25 (0.23), residues: 549 loop : -2.88 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 214 HIS 0.004 0.002 HIS C 21 PHE 0.026 0.002 PHE A 153 TYR 0.020 0.002 TYR A 310 ARG 0.004 0.001 ARG B 100 *********************** 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 fitting. rotamer outliers: 26 poor density : 209 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8520 (tt0) cc_final: 0.8005 (tt0) REVERT: A 210 LYS cc_start: 0.7762 (ttpt) cc_final: 0.7027 (ttmm) REVERT: A 290 ASP cc_start: 0.7287 (m-30) cc_final: 0.6608 (p0) REVERT: A 296 GLU cc_start: 0.7566 (tp30) cc_final: 0.7065 (tp30) REVERT: B 2 GLU cc_start: 0.7072 (tt0) cc_final: 0.6830 (tt0) REVERT: B 50 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7317 (mm-40) REVERT: B 62 GLU cc_start: 0.8386 (tt0) cc_final: 0.7924 (tt0) REVERT: B 114 MET cc_start: 0.7373 (mmm) cc_final: 0.7162 (mmm) REVERT: B 210 LYS cc_start: 0.7709 (ttpt) cc_final: 0.6906 (tppt) REVERT: B 219 LYS cc_start: 0.6951 (tttp) cc_final: 0.6682 (ttmt) REVERT: C 38 MET cc_start: 0.7704 (mtp) cc_final: 0.7422 (mmm) REVERT: C 62 GLU cc_start: 0.8407 (tt0) cc_final: 0.8020 (tt0) REVERT: C 210 LYS cc_start: 0.7671 (ttpt) cc_final: 0.7171 (ttmm) REVERT: C 224 ASN cc_start: 0.7840 (m-40) cc_final: 0.7517 (m-40) REVERT: C 312 ASP cc_start: 0.8353 (t0) cc_final: 0.8044 (t0) REVERT: C 329 ASP cc_start: 0.6324 (m-30) cc_final: 0.6085 (m-30) outliers start: 26 outliers final: 15 residues processed: 227 average time/residue: 0.1790 time to fit residues: 56.2124 Evaluate side-chains 210 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 195 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 0.0670 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8049 Z= 0.295 Angle : 0.632 7.057 10890 Z= 0.351 Chirality : 0.046 0.149 1104 Planarity : 0.004 0.038 1470 Dihedral : 5.787 40.384 1142 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.20 % Allowed : 17.49 % Favored : 77.31 % 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: -1.62 (0.26), residues: 1014 helix: -4.81 (0.17), residues: 18 sheet: 0.17 (0.22), residues: 558 loop : -2.67 (0.25), residues: 438 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 0.021 0.002 TYR A 310 ARG 0.003 0.001 ARG A 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 242 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 201 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7618 (mtmm) cc_final: 0.7150 (mtmm) REVERT: A 62 GLU cc_start: 0.8516 (tt0) cc_final: 0.8074 (tt0) REVERT: A 210 LYS cc_start: 0.7817 (ttpt) cc_final: 0.7118 (ttmm) REVERT: B 50 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7413 (mm-40) REVERT: B 62 GLU cc_start: 0.8385 (tt0) cc_final: 0.7973 (tt0) REVERT: B 157 TYR cc_start: 0.6903 (t80) cc_final: 0.6189 (t80) REVERT: B 210 LYS cc_start: 0.7782 (ttpt) cc_final: 0.6936 (tppt) REVERT: B 219 LYS cc_start: 0.6878 (tttp) cc_final: 0.6360 (tttt) REVERT: B 272 SER cc_start: 0.7334 (m) cc_final: 0.7104 (t) REVERT: C 62 GLU cc_start: 0.8476 (tt0) cc_final: 0.8078 (tt0) REVERT: C 210 LYS cc_start: 0.7588 (ttpt) cc_final: 0.7154 (ttmm) REVERT: C 329 ASP cc_start: 0.6369 (m-30) cc_final: 0.6102 (m-30) outliers start: 41 outliers final: 34 residues processed: 230 average time/residue: 0.1798 time to fit residues: 57.0702 Evaluate side-chains 226 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 56 THR 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 248 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 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 330 ASP 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 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8049 Z= 0.236 Angle : 0.587 7.059 10890 Z= 0.328 Chirality : 0.045 0.168 1104 Planarity : 0.004 0.038 1470 Dihedral : 5.421 27.513 1142 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.45 % Allowed : 20.15 % Favored : 74.40 % 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: -1.37 (0.26), residues: 1014 helix: -4.54 (0.20), residues: 18 sheet: 0.20 (0.22), residues: 582 loop : -2.43 (0.26), residues: 414 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 0.021 0.002 PHE A 128 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 246 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 203 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7644 (mtmm) cc_final: 0.7177 (mtmm) REVERT: A 62 GLU cc_start: 0.8524 (tt0) cc_final: 0.8081 (tt0) REVERT: A 210 LYS cc_start: 0.7739 (ttpt) cc_final: 0.7029 (ttmm) REVERT: B 62 GLU cc_start: 0.8395 (tt0) cc_final: 0.7998 (tt0) REVERT: B 157 TYR cc_start: 0.7027 (t80) cc_final: 0.6732 (t80) REVERT: B 210 LYS cc_start: 0.7812 (ttpt) cc_final: 0.6968 (tppt) REVERT: B 219 LYS cc_start: 0.6857 (tttp) cc_final: 0.6322 (tttt) REVERT: B 272 SER cc_start: 0.7298 (m) cc_final: 0.6993 (t) REVERT: C 62 GLU cc_start: 0.8487 (tt0) cc_final: 0.8098 (tt0) REVERT: C 210 LYS cc_start: 0.7585 (ttpt) cc_final: 0.7118 (ttmm) REVERT: C 329 ASP cc_start: 0.6585 (m-30) cc_final: 0.6324 (m-30) outliers start: 43 outliers final: 34 residues processed: 231 average time/residue: 0.1763 time to fit residues: 56.7603 Evaluate side-chains 233 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 199 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 56 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 39 THR 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 288 ASP Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 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 330 ASP Chi-restraints excluded: chain C residue 337 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 68 optimal weight: 0.0670 chunk 0 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN C 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8049 Z= 0.181 Angle : 0.547 7.108 10890 Z= 0.307 Chirality : 0.043 0.136 1104 Planarity : 0.003 0.039 1470 Dihedral : 5.036 20.671 1140 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.07 % Allowed : 21.93 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.26), residues: 1014 helix: -4.21 (0.26), residues: 18 sheet: 0.21 (0.22), residues: 558 loop : -2.33 (0.26), residues: 438 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 0.015 0.001 TYR A 310 ARG 0.001 0.000 ARG B 100 *********************** 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 239 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 199 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.7667 (mtmm) cc_final: 0.7193 (mtmm) REVERT: A 62 GLU cc_start: 0.8530 (tt0) cc_final: 0.8122 (tt0) REVERT: A 210 LYS cc_start: 0.7755 (ttpt) cc_final: 0.7044 (ttmm) REVERT: B 62 GLU cc_start: 0.8441 (tt0) cc_final: 0.8032 (tt0) REVERT: B 210 LYS cc_start: 0.7759 (ttpt) cc_final: 0.6955 (tppt) REVERT: B 272 SER cc_start: 0.7250 (m) cc_final: 0.6965 (t) REVERT: C 62 GLU cc_start: 0.8493 (tt0) cc_final: 0.8138 (tt0) REVERT: C 210 LYS cc_start: 0.7540 (ttpt) cc_final: 0.7162 (ttmm) outliers start: 40 outliers final: 35 residues processed: 224 average time/residue: 0.1761 time to fit residues: 54.8172 Evaluate side-chains 231 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 196 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 56 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 178 ILE Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 7 ASP 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 178 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 312 ASP Chi-restraints excluded: chain C residue 330 ASP 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 57 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 51 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 236 ASN B 141 ASN C 141 ASN C 223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 8049 Z= 0.468 Angle : 0.711 6.948 10890 Z= 0.396 Chirality : 0.049 0.147 1104 Planarity : 0.005 0.036 1470 Dihedral : 5.935 30.604 1140 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 7.10 % Allowed : 22.18 % 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: -3.69 (0.49), residues: 18 sheet: 0.50 (0.23), residues: 546 loop : -2.74 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 214 HIS 0.003 0.002 HIS A 21 PHE 0.020 0.003 PHE A 145 TYR 0.024 0.002 TYR B 157 ARG 0.004 0.001 ARG B 100 *********************** 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 246 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 190 time to evaluate : 0.868 Fit side-chains REVERT: A 25 LYS cc_start: 0.7649 (mtmm) cc_final: 0.7170 (mtmm) REVERT: A 62 GLU cc_start: 0.8534 (tt0) cc_final: 0.8062 (tt0) REVERT: A 141 ASN cc_start: 0.6167 (OUTLIER) cc_final: 0.5569 (t0) REVERT: A 187 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7343 (tt) REVERT: A 210 LYS cc_start: 0.7708 (ttpt) cc_final: 0.7067 (ttmm) REVERT: B 62 GLU cc_start: 0.8374 (tt0) cc_final: 0.7957 (tt0) REVERT: B 210 LYS cc_start: 0.7711 (ttpt) cc_final: 0.6774 (tppt) REVERT: B 219 LYS cc_start: 0.6980 (tttp) cc_final: 0.6733 (ttmt) REVERT: C 38 MET cc_start: 0.7883 (mtp) cc_final: 0.7587 (ttm) REVERT: C 62 GLU cc_start: 0.8524 (tt0) cc_final: 0.8119 (tt0) REVERT: C 141 ASN cc_start: 0.6575 (OUTLIER) cc_final: 0.6320 (t0) REVERT: C 210 LYS cc_start: 0.7463 (ttpt) cc_final: 0.7069 (ttmm) REVERT: C 296 GLU cc_start: 0.7832 (tp30) cc_final: 0.7102 (tp30) REVERT: C 314 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6402 (mm) outliers start: 56 outliers final: 39 residues processed: 231 average time/residue: 0.1789 time to fit residues: 57.1023 Evaluate side-chains 230 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 187 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP 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 56 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 141 ASN Chi-restraints excluded: chain A residue 187 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 337 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 39 THR 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 209 LYS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 141 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 314 ILE Chi-restraints excluded: chain C residue 330 ASP 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 72 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.0980 chunk 39 optimal weight: 0.0870 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN C 141 ASN C 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2861 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= 0.212 Angle : 0.577 7.318 10890 Z= 0.325 Chirality : 0.044 0.184 1104 Planarity : 0.003 0.039 1470 Dihedral : 5.313 23.362 1140 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.96 % Allowed : 24.08 % Favored : 69.96 % 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: -1.28 (0.26), residues: 1014 helix: -3.35 (0.58), residues: 18 sheet: 0.15 (0.22), residues: 588 loop : -2.27 (0.26), residues: 408 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 0.021 0.002 PHE A 128 TYR 0.016 0.001 TYR A 310 ARG 0.001 0.000 ARG B 100 *********************** 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 238 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 191 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8544 (tt0) cc_final: 0.8112 (tt0) REVERT: A 187 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7251 (tt) REVERT: A 210 LYS cc_start: 0.7698 (ttpt) cc_final: 0.7049 (ttmm) REVERT: B 62 GLU cc_start: 0.8388 (tt0) cc_final: 0.7977 (tt0) REVERT: B 182 TYR cc_start: 0.7993 (t80) cc_final: 0.7668 (t80) REVERT: B 210 LYS cc_start: 0.7801 (ttpt) cc_final: 0.6899 (tppt) REVERT: B 272 SER cc_start: 0.7229 (m) cc_final: 0.6903 (t) REVERT: C 62 GLU cc_start: 0.8537 (tt0) cc_final: 0.8141 (tt0) REVERT: C 210 LYS cc_start: 0.7507 (ttpt) cc_final: 0.7112 (ttmm) outliers start: 47 outliers final: 39 residues processed: 224 average time/residue: 0.1766 time to fit residues: 55.1805 Evaluate side-chains 234 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 194 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 187 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 337 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 13 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 209 LYS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 288 ASP 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 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 330 ASP 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 19 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 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 C 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8049 Z= 0.323 Angle : 0.632 7.184 10890 Z= 0.353 Chirality : 0.046 0.176 1104 Planarity : 0.004 0.038 1470 Dihedral : 5.613 25.392 1140 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 6.21 % Allowed : 24.08 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.27 (0.26), residues: 1014 helix: -3.16 (0.69), residues: 18 sheet: 0.41 (0.23), residues: 555 loop : -2.51 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 214 HIS 0.003 0.002 HIS C 21 PHE 0.020 0.002 PHE B 128 TYR 0.018 0.002 TYR A 310 ARG 0.002 0.000 ARG B 100 *********************** 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 234 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 185 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8545 (tt0) cc_final: 0.8096 (tt0) REVERT: A 187 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7274 (tt) REVERT: A 210 LYS cc_start: 0.7714 (ttpt) cc_final: 0.7077 (ttmm) REVERT: B 62 GLU cc_start: 0.8379 (tt0) cc_final: 0.7976 (tt0) REVERT: B 210 LYS cc_start: 0.7711 (ttpt) cc_final: 0.6770 (tppt) REVERT: C 62 GLU cc_start: 0.8533 (tt0) cc_final: 0.8127 (tt0) REVERT: C 115 LEU cc_start: 0.8383 (mp) cc_final: 0.8172 (mp) REVERT: C 210 LYS cc_start: 0.7635 (ttpt) cc_final: 0.7227 (ttmm) outliers start: 49 outliers final: 44 residues processed: 220 average time/residue: 0.1866 time to fit residues: 57.3024 Evaluate side-chains 230 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 185 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP 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 56 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 187 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 337 VAL Chi-restraints excluded: chain B residue 7 ASP 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 209 LYS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 288 ASP 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 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 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 296 GLU Chi-restraints excluded: chain C residue 330 ASP 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 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2969 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= 0.316 Angle : 0.633 7.172 10890 Z= 0.354 Chirality : 0.046 0.160 1104 Planarity : 0.004 0.038 1470 Dihedral : 5.586 24.663 1140 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 6.97 % Allowed : 23.32 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.31 (0.26), residues: 1014 helix: -3.05 (0.73), residues: 18 sheet: 0.30 (0.23), residues: 555 loop : -2.39 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 214 HIS 0.003 0.002 HIS C 21 PHE 0.021 0.002 PHE A 153 TYR 0.017 0.002 TYR A 310 ARG 0.002 0.000 ARG B 100 *********************** 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 238 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 183 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8549 (tt0) cc_final: 0.8109 (tt0) REVERT: A 187 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7269 (tt) REVERT: A 210 LYS cc_start: 0.7745 (ttpt) cc_final: 0.7085 (ttmm) REVERT: B 29 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7104 (pm20) REVERT: B 62 GLU cc_start: 0.8376 (tt0) cc_final: 0.7949 (tt0) REVERT: B 210 LYS cc_start: 0.7712 (ttpt) cc_final: 0.6771 (tppt) REVERT: C 62 GLU cc_start: 0.8533 (tt0) cc_final: 0.8131 (tt0) REVERT: C 210 LYS cc_start: 0.7468 (ttpt) cc_final: 0.7077 (ttmm) outliers start: 55 outliers final: 46 residues processed: 223 average time/residue: 0.1786 time to fit residues: 55.3066 Evaluate side-chains 233 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 185 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP 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 56 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 187 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 337 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 29 GLU 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 288 ASP 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 336 ILE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 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 256 ASP Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 330 ASP 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 101 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.0040 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2948 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 : 0.584 7.172 10890 Z= 0.328 Chirality : 0.045 0.149 1104 Planarity : 0.003 0.039 1470 Dihedral : 5.296 23.073 1140 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 6.21 % Allowed : 24.08 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.26), residues: 1014 helix: -3.06 (0.69), residues: 18 sheet: 0.16 (0.22), residues: 585 loop : -2.20 (0.26), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 214 HIS 0.003 0.001 HIS C 21 PHE 0.022 0.002 PHE A 153 TYR 0.016 0.001 TYR A 310 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 244 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 195 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 62 GLU cc_start: 0.8552 (tt0) cc_final: 0.8085 (tt0) REVERT: A 187 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.7219 (tt) REVERT: A 210 LYS cc_start: 0.7691 (ttpt) cc_final: 0.7047 (ttmm) REVERT: B 29 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7114 (pm20) REVERT: B 62 GLU cc_start: 0.8390 (tt0) cc_final: 0.7986 (tt0) REVERT: B 210 LYS cc_start: 0.7793 (ttpt) cc_final: 0.6940 (tppt) REVERT: C 2 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6557 (tp30) REVERT: C 62 GLU cc_start: 0.8536 (tt0) cc_final: 0.8153 (tt0) REVERT: C 115 LEU cc_start: 0.8378 (mp) cc_final: 0.8166 (mp) REVERT: C 182 TYR cc_start: 0.8008 (t80) cc_final: 0.7595 (t80) REVERT: C 210 LYS cc_start: 0.7484 (ttpt) cc_final: 0.7106 (ttmm) outliers start: 49 outliers final: 42 residues processed: 224 average time/residue: 0.1745 time to fit residues: 54.3141 Evaluate side-chains 234 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 189 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP 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 56 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 187 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 337 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 29 GLU 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 288 ASP 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 337 VAL Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 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 256 ASP Chi-restraints excluded: chain C residue 330 ASP 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 22 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.161521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.153673 restraints weight = 9020.644| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.16 r_work: 0.3594 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3012 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= 0.342 Angle : 0.650 7.219 10890 Z= 0.363 Chirality : 0.047 0.154 1104 Planarity : 0.004 0.038 1470 Dihedral : 5.646 25.840 1140 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 6.46 % Allowed : 23.95 % Favored : 69.58 % 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: -1.26 (0.25), residues: 1014 helix: -2.93 (0.75), residues: 18 sheet: 0.36 (0.22), residues: 561 loop : -2.45 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 214 HIS 0.003 0.002 HIS C 21 PHE 0.022 0.002 PHE A 153 TYR 0.018 0.002 TYR A 310 ARG 0.002 0.001 ARG A 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2160.95 seconds wall clock time: 40 minutes 11.46 seconds (2411.46 seconds total)