Starting phenix.real_space_refine on Wed Feb 14 08:45:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce5_16599/02_2024/8ce5_16599_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce5_16599/02_2024/8ce5_16599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce5_16599/02_2024/8ce5_16599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce5_16599/02_2024/8ce5_16599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce5_16599/02_2024/8ce5_16599_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ce5_16599/02_2024/8ce5_16599_updated.pdb" } resolution = 3.62 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= 0.001 sd= 0.043 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 42 5.16 5 C 5847 2.51 5 N 1550 2.21 5 O 1532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "a GLU 5": "OE1" <-> "OE2" Residue "a PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 95": "OE1" <-> "OE2" Residue "b GLU 20": "OE1" <-> "OE2" Residue "b GLU 67": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8979 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1587 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1656 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 202} Chain: "C" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1930 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 491 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "a" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1595 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 6, 'TRANS': 196} Chain: "b" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1656 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 202} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.31, per 1000 atoms: 0.59 Number of scatterers: 8979 At special positions: 0 Unit cell: (102.726, 75.508, 108.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 6 15.00 Mg 2 11.99 O 1532 8.00 N 1550 7.00 C 5847 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: 3.53 Conformation dependent library (CDL) restraints added in 1.8 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 6 sheets defined 61.2% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 71 through 76 Processing helix chain 'A' and resid 93 through 99 Processing helix chain 'A' and resid 111 through 114 No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.889A pdb=" N ALA A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 176 removed outlier: 3.990A pdb=" N ASP A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 20 through 39 Proline residue: B 24 - end of helix Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 43 through 76 removed outlier: 3.837A pdb=" N ALA B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) Proline residue: B 51 - end of helix removed outlier: 4.101A pdb=" N GLU B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ARG B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N PHE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU B 74 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 84 removed outlier: 4.095A pdb=" N LEU B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 117 removed outlier: 4.522A pdb=" N LEU B 106 " --> pdb=" O MET B 102 " (cutoff:3.500A) Proline residue: B 107 - end of helix Proline residue: B 113 - end of helix Processing helix chain 'B' and resid 123 through 150 Proline residue: B 138 - end of helix Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 159 through 184 Proline residue: B 167 - end of helix Proline residue: B 171 - end of helix Processing helix chain 'B' and resid 190 through 219 Proline residue: B 208 - end of helix removed outlier: 3.804A pdb=" N ALA B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 7 No H-bonds generated for 'chain 'C' and resid 4 through 7' Processing helix chain 'C' and resid 11 through 41 Proline residue: C 23 - end of helix Processing helix chain 'C' and resid 54 through 82 removed outlier: 3.916A pdb=" N HIS C 60 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Proline residue: C 62 - end of helix removed outlier: 5.394A pdb=" N PHE C 79 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 114 removed outlier: 4.166A pdb=" N ALA C 92 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Proline residue: C 98 - end of helix Processing helix chain 'C' and resid 116 through 119 No H-bonds generated for 'chain 'C' and resid 116 through 119' Processing helix chain 'C' and resid 129 through 148 Processing helix chain 'C' and resid 153 through 182 Proline residue: C 171 - end of helix removed outlier: 3.646A pdb=" N GLU C 178 " --> pdb=" O HIS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 228 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'D' and resid 8 through 12 Processing helix chain 'D' and resid 18 through 62 Proline residue: D 31 - end of helix removed outlier: 3.699A pdb=" N SER D 39 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS D 43 " --> pdb=" O SER D 39 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG D 56 " --> pdb=" O GLN D 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 50 Processing helix chain 'a' and resid 71 through 74 No H-bonds generated for 'chain 'a' and resid 71 through 74' Processing helix chain 'a' and resid 93 through 99 Processing helix chain 'a' and resid 112 through 115 No H-bonds generated for 'chain 'a' and resid 112 through 115' Processing helix chain 'a' and resid 131 through 143 removed outlier: 3.628A pdb=" N ALA a 138 " --> pdb=" O GLN a 134 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG a 141 " --> pdb=" O VAL a 137 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU a 142 " --> pdb=" O ALA a 138 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TRP a 143 " --> pdb=" O LEU a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 161 through 176 Processing helix chain 'b' and resid 3 through 14 Processing helix chain 'b' and resid 22 through 39 removed outlier: 3.551A pdb=" N PHE b 28 " --> pdb=" O PRO b 24 " (cutoff:3.500A) Proline residue: b 36 - end of helix Processing helix chain 'b' and resid 43 through 69 Proline residue: b 51 - end of helix removed outlier: 4.091A pdb=" N GLU b 67 " --> pdb=" O LEU b 63 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ARG b 68 " --> pdb=" O LEU b 64 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU b 69 " --> pdb=" O ALA b 65 " (cutoff:3.500A) Processing helix chain 'b' and resid 71 through 76 removed outlier: 3.788A pdb=" N GLN b 75 " --> pdb=" O ARG b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 83 Processing helix chain 'b' and resid 89 through 118 removed outlier: 4.426A pdb=" N LEU b 106 " --> pdb=" O MET b 102 " (cutoff:3.500A) Proline residue: b 107 - end of helix Proline residue: b 113 - end of helix Processing helix chain 'b' and resid 123 through 152 Proline residue: b 138 - end of helix Proline residue: b 146 - end of helix Processing helix chain 'b' and resid 159 through 162 No H-bonds generated for 'chain 'b' and resid 159 through 162' Processing helix chain 'b' and resid 167 through 184 removed outlier: 3.599A pdb=" N ILE b 170 " --> pdb=" O PRO b 167 " (cutoff:3.500A) Proline residue: b 171 - end of helix removed outlier: 3.507A pdb=" N ALA b 176 " --> pdb=" O LEU b 173 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR b 177 " --> pdb=" O ILE b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 218 removed outlier: 3.652A pdb=" N ILE b 195 " --> pdb=" O GLY b 191 " (cutoff:3.500A) Proline residue: b 208 - end of helix removed outlier: 3.641A pdb=" N ALA b 213 " --> pdb=" O PHE b 209 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 5 through 7 Processing sheet with id= B, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.489A pdb=" N VAL A 181 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'a' and resid 24 through 26 removed outlier: 4.034A pdb=" N LEU a 4 " --> pdb=" O LEU a 26 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'a' and resid 32 through 34 removed outlier: 6.485A pdb=" N ARG a 197 " --> pdb=" O GLN a 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'a' and resid 78 through 81 removed outlier: 6.884A pdb=" N LEU a 149 " --> pdb=" O LEU a 79 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE a 81 " --> pdb=" O LEU a 149 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE a 151 " --> pdb=" O ILE a 81 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE a 180 " --> pdb=" O TRP a 150 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU a 152 " --> pdb=" O ILE a 180 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE a 182 " --> pdb=" O LEU a 152 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'a' and resid 9 through 11 removed outlier: 7.353A pdb=" N CYS a 11 " --> pdb=" O SER a 20 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N SER a 20 " --> pdb=" O CYS a 11 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1236 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: 2.33 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 9 1.22 - 1.37: 2973 1.37 - 1.52: 3175 1.52 - 1.67: 2960 1.67 - 1.82: 79 Bond restraints: 9196 Sorted by residual: bond pdb=" N ASP A 153 " pdb=" CA ASP A 153 " ideal model delta sigma weight residual 1.453 1.333 0.121 1.22e-02 6.72e+03 9.77e+01 bond pdb=" CG PRO b 43 " pdb=" CD PRO b 43 " ideal model delta sigma weight residual 1.503 1.196 0.307 3.40e-02 8.65e+02 8.14e+01 bond pdb=" CB PRO b 43 " pdb=" CG PRO b 43 " ideal model delta sigma weight residual 1.492 1.070 0.422 5.00e-02 4.00e+02 7.12e+01 bond pdb=" C4 ATP A 303 " pdb=" C5 ATP A 303 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.08e+01 bond pdb=" C4 ATP A 302 " pdb=" C5 ATP A 302 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.61e+01 ... (remaining 9191 not shown) Histogram of bond angle deviations from ideal: 73.41 - 94.69: 2 94.69 - 115.97: 6110 115.97 - 137.26: 6447 137.26 - 158.54: 1 158.54 - 179.82: 1 Bond angle restraints: 12561 Sorted by residual: angle pdb=" PB ATP A 302 " pdb=" O3B ATP A 302 " pdb=" PG ATP A 302 " ideal model delta sigma weight residual 139.87 109.91 29.96 1.00e+00 1.00e+00 8.97e+02 angle pdb=" CB PRO b 43 " pdb=" CG PRO b 43 " pdb=" CD PRO b 43 " ideal model delta sigma weight residual 106.10 179.82 -73.72 3.20e+00 9.77e-02 5.31e+02 angle pdb=" PB ATP A 303 " pdb=" O3B ATP A 303 " pdb=" PG ATP A 303 " ideal model delta sigma weight residual 139.87 117.97 21.90 1.00e+00 1.00e+00 4.80e+02 angle pdb=" PA ATP A 302 " pdb=" O3A ATP A 302 " pdb=" PB ATP A 302 " ideal model delta sigma weight residual 136.83 115.48 21.35 1.00e+00 1.00e+00 4.56e+02 angle pdb=" PA ATP A 303 " pdb=" O3A ATP A 303 " pdb=" PB ATP A 303 " ideal model delta sigma weight residual 136.83 115.64 21.19 1.00e+00 1.00e+00 4.49e+02 ... (remaining 12556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4566 17.71 - 35.42: 630 35.42 - 53.13: 176 53.13 - 70.84: 33 70.84 - 88.55: 19 Dihedral angle restraints: 5424 sinusoidal: 2154 harmonic: 3270 Sorted by residual: dihedral pdb=" CA LEU A 78 " pdb=" C LEU A 78 " pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA HIS C 60 " pdb=" C HIS C 60 " pdb=" N VAL C 61 " pdb=" CA VAL C 61 " ideal model delta harmonic sigma weight residual 180.00 -153.81 -26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA VAL C 76 " pdb=" C VAL C 76 " pdb=" N ALA C 77 " pdb=" CA ALA C 77 " ideal model delta harmonic sigma weight residual 180.00 157.45 22.55 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 5421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1449 0.125 - 0.250: 31 0.250 - 0.374: 1 0.374 - 0.499: 0 0.499 - 0.624: 2 Chirality restraints: 1483 Sorted by residual: chirality pdb=" CG LEU b 108 " pdb=" CB LEU b 108 " pdb=" CD1 LEU b 108 " pdb=" CD2 LEU b 108 " both_signs ideal model delta sigma weight residual False -2.59 -1.97 -0.62 2.00e-01 2.50e+01 9.73e+00 chirality pdb=" CB ILE A 124 " pdb=" CA ILE A 124 " pdb=" CG1 ILE A 124 " pdb=" CG2 ILE A 124 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.55 2.00e-01 2.50e+01 7.46e+00 chirality pdb=" CB THR b 169 " pdb=" CA THR b 169 " pdb=" OG1 THR b 169 " pdb=" CG2 THR b 169 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1480 not shown) Planarity restraints: 1547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 112 " 0.104 5.00e-02 4.00e+02 1.46e-01 3.43e+01 pdb=" N PRO B 113 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU b 166 " 0.095 5.00e-02 4.00e+02 1.39e-01 3.11e+01 pdb=" N PRO b 167 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO b 167 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO b 167 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU b 42 " -0.061 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO b 43 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO b 43 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO b 43 " -0.045 5.00e-02 4.00e+02 ... (remaining 1544 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 107 2.64 - 3.20: 7814 3.20 - 3.77: 14579 3.77 - 4.33: 18555 4.33 - 4.90: 30602 Nonbonded interactions: 71657 Sorted by model distance: nonbonded pdb=" OG1 THR a 43 " pdb="MG MG a 301 " model vdw 2.072 2.170 nonbonded pdb="MG MG A 301 " pdb=" O3G ATP A 302 " model vdw 2.203 2.170 nonbonded pdb=" OG1 THR A 43 " pdb="MG MG A 301 " model vdw 2.228 2.170 nonbonded pdb=" OG1 THR A 92 " pdb=" OE1 GLU A 95 " model vdw 2.254 2.440 nonbonded pdb=" NH1 ARG a 16 " pdb=" O GLY a 39 " model vdw 2.263 2.520 ... (remaining 71652 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' and (resid 2 through 203 or resid 301)) selection = (chain 'a' and (resid 2 through 203 or resid 301)) } ncs_group { reference = chain 'B' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.430 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 29.030 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 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 : 0.008 0.422 9196 Z= 0.525 Angle : 1.417 73.718 12561 Z= 0.803 Chirality : 0.054 0.624 1483 Planarity : 0.010 0.146 1547 Dihedral : 18.252 88.553 3310 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.14 % Favored : 95.50 % Rotamer: Outliers : 0.32 % Allowed : 27.45 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.59 (0.24), residues: 1134 helix: -0.42 (0.18), residues: 715 sheet: -2.41 (0.75), residues: 45 loop : -1.94 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 122 HIS 0.007 0.001 HIS A 83 PHE 0.036 0.002 PHE b 28 TYR 0.034 0.002 TYR C 58 ARG 0.008 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 146 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 179 TRP cc_start: 0.7688 (t60) cc_final: 0.7372 (t60) REVERT: a 195 LYS cc_start: 0.7429 (ptpp) cc_final: 0.6883 (tppt) outliers start: 3 outliers final: 2 residues processed: 147 average time/residue: 0.2205 time to fit residues: 44.5032 Evaluate side-chains 141 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 43 THR Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.0170 chunk 101 optimal weight: 0.8980 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN C 7 GLN C 49 GLN C 52 ASN C 169 ASN a 101 HIS a 127 ASN b 23 ASN b 81 GLN b 100 HIS b 220 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9196 Z= 0.244 Angle : 0.666 9.538 12561 Z= 0.327 Chirality : 0.042 0.265 1483 Planarity : 0.007 0.088 1547 Dihedral : 10.427 84.489 1299 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.97 % Favored : 95.86 % Rotamer: Outliers : 3.77 % Allowed : 25.94 % Favored : 70.29 % 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: -0.58 (0.25), residues: 1134 helix: 0.41 (0.20), residues: 711 sheet: -2.61 (0.70), residues: 50 loop : -1.50 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 84 HIS 0.002 0.001 HIS A 83 PHE 0.014 0.001 PHE b 28 TYR 0.009 0.001 TYR A 100 ARG 0.003 0.000 ARG a 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: B 85 LEU cc_start: 0.7573 (mt) cc_final: 0.7258 (mt) REVERT: C 80 ILE cc_start: 0.8031 (tp) cc_final: 0.7791 (tp) REVERT: a 195 LYS cc_start: 0.7442 (ptpp) cc_final: 0.7045 (tppt) outliers start: 35 outliers final: 19 residues processed: 178 average time/residue: 0.2223 time to fit residues: 53.9673 Evaluate side-chains 161 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 181 VAL Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 123 VAL Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 184 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 83 HIS ** a 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 HIS ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9196 Z= 0.320 Angle : 0.692 10.553 12561 Z= 0.339 Chirality : 0.043 0.281 1483 Planarity : 0.006 0.075 1547 Dihedral : 9.821 81.170 1296 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.85 % Favored : 94.97 % Rotamer: Outliers : 5.06 % Allowed : 26.05 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1134 helix: 0.45 (0.20), residues: 720 sheet: -2.71 (0.68), residues: 50 loop : -1.41 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 180 HIS 0.009 0.001 HIS C 184 PHE 0.014 0.002 PHE a 156 TYR 0.011 0.002 TYR C 58 ARG 0.005 0.000 ARG a 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 149 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 88 LYS cc_start: 0.7374 (mmtm) cc_final: 0.7010 (mmtt) REVERT: C 80 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8076 (tp) REVERT: a 156 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.6759 (m-80) REVERT: a 195 LYS cc_start: 0.7659 (ptpp) cc_final: 0.6984 (tppt) REVERT: b 101 TRP cc_start: 0.7527 (t60) cc_final: 0.7296 (t60) outliers start: 47 outliers final: 25 residues processed: 180 average time/residue: 0.2200 time to fit residues: 53.7825 Evaluate side-chains 168 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 80 TRP Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain a residue 156 PHE Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain b residue 61 SER Chi-restraints excluded: chain b residue 68 ARG Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 170 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.0870 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 154 GLN a 186 HIS ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9196 Z= 0.228 Angle : 0.623 10.404 12561 Z= 0.304 Chirality : 0.041 0.325 1483 Planarity : 0.006 0.070 1547 Dihedral : 9.683 83.766 1296 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.94 % Rotamer: Outliers : 4.09 % Allowed : 27.88 % Favored : 68.03 % 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: -0.07 (0.26), residues: 1134 helix: 0.75 (0.20), residues: 721 sheet: -2.52 (0.70), residues: 50 loop : -1.16 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 179 HIS 0.004 0.001 HIS B 17 PHE 0.027 0.001 PHE A 24 TYR 0.010 0.001 TYR C 58 ARG 0.004 0.000 ARG a 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 144 time to evaluate : 1.044 Fit side-chains REVERT: A 5 GLU cc_start: 0.6537 (mp0) cc_final: 0.6115 (mp0) REVERT: C 80 ILE cc_start: 0.8364 (tp) cc_final: 0.8126 (tp) REVERT: a 195 LYS cc_start: 0.7712 (ptpp) cc_final: 0.7047 (tppt) REVERT: b 101 TRP cc_start: 0.7554 (t60) cc_final: 0.7299 (t60) outliers start: 38 outliers final: 29 residues processed: 172 average time/residue: 0.2082 time to fit residues: 49.6513 Evaluate side-chains 164 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 184 SER Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 115 GLN a 186 HIS ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9196 Z= 0.439 Angle : 0.775 9.247 12561 Z= 0.377 Chirality : 0.047 0.384 1483 Planarity : 0.006 0.066 1547 Dihedral : 9.783 84.408 1296 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.64 % Favored : 94.27 % Rotamer: Outliers : 7.64 % Allowed : 26.16 % Favored : 66.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.51 (0.25), residues: 1134 helix: 0.33 (0.19), residues: 727 sheet: -2.54 (0.70), residues: 50 loop : -1.20 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 66 HIS 0.005 0.001 HIS D 38 PHE 0.026 0.002 PHE A 24 TYR 0.010 0.002 TYR C 15 ARG 0.005 0.001 ARG a 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 151 time to evaluate : 1.007 Fit side-chains REVERT: A 88 LYS cc_start: 0.7514 (mmtm) cc_final: 0.7160 (mmtp) REVERT: A 102 ARG cc_start: 0.7571 (mmp-170) cc_final: 0.7268 (mmp-170) REVERT: A 193 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6429 (tm-30) REVERT: B 17 HIS cc_start: 0.7159 (t-90) cc_final: 0.6949 (t-90) REVERT: C 80 ILE cc_start: 0.8539 (tp) cc_final: 0.8285 (tp) REVERT: C 221 MET cc_start: 0.7829 (tpt) cc_final: 0.7452 (ttt) REVERT: a 16 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.5407 (ttp-110) REVERT: a 49 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7858 (mp) REVERT: a 154 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7098 (mm110) REVERT: a 156 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.6574 (m-10) REVERT: a 193 GLU cc_start: 0.7698 (tp30) cc_final: 0.7324 (tp30) REVERT: b 101 TRP cc_start: 0.7716 (t60) cc_final: 0.7482 (t60) outliers start: 71 outliers final: 43 residues processed: 206 average time/residue: 0.2099 time to fit residues: 59.5622 Evaluate side-chains 192 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 145 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain a residue 5 GLU Chi-restraints excluded: chain a residue 16 ARG Chi-restraints excluded: chain a residue 43 THR Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 154 GLN Chi-restraints excluded: chain a residue 156 PHE Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 189 LEU Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain b residue 61 SER Chi-restraints excluded: chain b residue 68 ARG Chi-restraints excluded: chain b residue 109 LEU Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 184 SER Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 HIS ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9196 Z= 0.210 Angle : 0.637 9.317 12561 Z= 0.312 Chirality : 0.040 0.223 1483 Planarity : 0.006 0.064 1547 Dihedral : 9.634 86.434 1296 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 4.31 % Allowed : 29.60 % Favored : 66.09 % 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: -0.03 (0.26), residues: 1134 helix: 0.81 (0.20), residues: 724 sheet: -2.26 (0.75), residues: 50 loop : -1.30 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 101 HIS 0.003 0.001 HIS D 38 PHE 0.034 0.001 PHE A 24 TYR 0.010 0.001 TYR a 100 ARG 0.003 0.000 ARG a 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 1.048 Fit side-chains REVERT: A 5 GLU cc_start: 0.6446 (mp0) cc_final: 0.6041 (mp0) REVERT: B 17 HIS cc_start: 0.7031 (t-90) cc_final: 0.6750 (t-170) REVERT: B 63 LEU cc_start: 0.7808 (tp) cc_final: 0.7438 (tp) REVERT: C 17 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6693 (mt) REVERT: C 80 ILE cc_start: 0.8451 (tp) cc_final: 0.8187 (tp) REVERT: C 221 MET cc_start: 0.7841 (tpt) cc_final: 0.7378 (ttt) REVERT: D 54 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.4510 (tpm170) REVERT: a 16 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5224 (ttp-110) REVERT: a 193 GLU cc_start: 0.7745 (tp30) cc_final: 0.7258 (tp30) REVERT: b 101 TRP cc_start: 0.7549 (t60) cc_final: 0.7285 (t60) outliers start: 40 outliers final: 24 residues processed: 176 average time/residue: 0.2117 time to fit residues: 51.5531 Evaluate side-chains 168 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain a residue 16 ARG Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 184 SER Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 HIS ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9196 Z= 0.259 Angle : 0.656 9.447 12561 Z= 0.318 Chirality : 0.041 0.244 1483 Planarity : 0.006 0.063 1547 Dihedral : 9.531 86.458 1296 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.59 % Favored : 95.33 % Rotamer: Outliers : 4.41 % Allowed : 29.82 % Favored : 65.77 % 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: 0.04 (0.26), residues: 1134 helix: 0.85 (0.20), residues: 724 sheet: -2.28 (0.74), residues: 50 loop : -1.21 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 179 HIS 0.003 0.001 HIS C 184 PHE 0.032 0.001 PHE A 24 TYR 0.010 0.001 TYR a 100 ARG 0.003 0.000 ARG a 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 1.039 Fit side-chains REVERT: A 5 GLU cc_start: 0.6487 (mp0) cc_final: 0.6076 (mp0) REVERT: B 17 HIS cc_start: 0.7105 (t-90) cc_final: 0.6899 (t-90) REVERT: B 63 LEU cc_start: 0.7773 (tp) cc_final: 0.7339 (tp) REVERT: B 85 LEU cc_start: 0.7617 (mt) cc_final: 0.7197 (mt) REVERT: C 80 ILE cc_start: 0.8450 (tp) cc_final: 0.8217 (tp) REVERT: C 221 MET cc_start: 0.7815 (tpt) cc_final: 0.7380 (ttt) REVERT: D 54 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.4599 (ttm170) REVERT: a 16 ARG cc_start: 0.6284 (OUTLIER) cc_final: 0.5400 (ttp-110) REVERT: b 101 TRP cc_start: 0.7594 (t60) cc_final: 0.7333 (t60) outliers start: 41 outliers final: 28 residues processed: 170 average time/residue: 0.2205 time to fit residues: 51.3911 Evaluate side-chains 168 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain a residue 16 ARG Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 184 SER Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 190 ASN ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9196 Z= 0.368 Angle : 0.735 11.659 12561 Z= 0.354 Chirality : 0.045 0.407 1483 Planarity : 0.006 0.063 1547 Dihedral : 9.549 85.845 1296 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.20 % Favored : 94.71 % Rotamer: Outliers : 4.84 % Allowed : 29.82 % Favored : 65.34 % 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: -0.23 (0.26), residues: 1134 helix: 0.59 (0.20), residues: 726 sheet: -2.47 (0.71), residues: 50 loop : -1.20 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 179 HIS 0.004 0.001 HIS C 184 PHE 0.032 0.002 PHE A 24 TYR 0.009 0.001 TYR a 100 ARG 0.004 0.001 ARG b 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 149 time to evaluate : 0.966 Fit side-chains REVERT: A 88 LYS cc_start: 0.7470 (mmtm) cc_final: 0.7160 (mmtt) REVERT: A 193 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6371 (tm-30) REVERT: B 63 LEU cc_start: 0.7839 (tp) cc_final: 0.7364 (tp) REVERT: C 17 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7090 (mt) REVERT: C 80 ILE cc_start: 0.8530 (tp) cc_final: 0.8297 (tp) REVERT: C 221 MET cc_start: 0.7837 (tpt) cc_final: 0.7432 (ttt) REVERT: D 54 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.4620 (ttm170) REVERT: a 16 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.5509 (ttp-110) REVERT: a 49 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7811 (mp) REVERT: a 193 GLU cc_start: 0.7774 (tp30) cc_final: 0.7354 (tp30) REVERT: b 101 TRP cc_start: 0.7777 (t60) cc_final: 0.7503 (t60) outliers start: 45 outliers final: 29 residues processed: 179 average time/residue: 0.2149 time to fit residues: 52.8773 Evaluate side-chains 182 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 149 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain a residue 16 ARG Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 184 SER Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 66 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 HIS a 190 ASN ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9196 Z= 0.214 Angle : 0.649 10.820 12561 Z= 0.315 Chirality : 0.041 0.325 1483 Planarity : 0.005 0.062 1547 Dihedral : 9.467 86.625 1296 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.94 % Rotamer: Outliers : 3.23 % Allowed : 31.11 % Favored : 65.66 % 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: 0.07 (0.26), residues: 1134 helix: 0.92 (0.20), residues: 726 sheet: -2.42 (0.71), residues: 50 loop : -1.30 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 179 HIS 0.003 0.001 HIS D 38 PHE 0.034 0.001 PHE A 24 TYR 0.009 0.001 TYR a 100 ARG 0.004 0.000 ARG a 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: B 63 LEU cc_start: 0.7758 (tp) cc_final: 0.7347 (tp) REVERT: B 85 LEU cc_start: 0.7557 (mt) cc_final: 0.7079 (mt) REVERT: C 80 ILE cc_start: 0.8471 (tp) cc_final: 0.8242 (tp) REVERT: C 221 MET cc_start: 0.7786 (tpt) cc_final: 0.7319 (ttt) REVERT: D 54 ARG cc_start: 0.6814 (OUTLIER) cc_final: 0.4721 (ttm170) REVERT: a 16 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5311 (ttp-110) REVERT: a 193 GLU cc_start: 0.7729 (tp30) cc_final: 0.7272 (tp30) REVERT: b 101 TRP cc_start: 0.7691 (t60) cc_final: 0.7417 (t60) outliers start: 30 outliers final: 27 residues processed: 165 average time/residue: 0.2178 time to fit residues: 49.3142 Evaluate side-chains 172 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 38 HIS Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain a residue 16 ARG Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 184 SER Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 0.0070 chunk 88 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 94 optimal weight: 0.0470 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS ** a 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 HIS ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9196 Z= 0.195 Angle : 0.638 10.330 12561 Z= 0.308 Chirality : 0.040 0.293 1483 Planarity : 0.005 0.061 1547 Dihedral : 9.332 86.030 1296 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.70 % Favored : 96.21 % Rotamer: Outliers : 3.23 % Allowed : 31.43 % Favored : 65.34 % 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: 0.35 (0.26), residues: 1134 helix: 1.12 (0.20), residues: 726 sheet: -2.37 (0.70), residues: 50 loop : -1.13 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 179 HIS 0.003 0.001 HIS C 60 PHE 0.032 0.001 PHE A 24 TYR 0.009 0.001 TYR a 100 ARG 0.003 0.000 ARG B 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 1.190 Fit side-chains REVERT: A 5 GLU cc_start: 0.6567 (mp0) cc_final: 0.6157 (mp0) REVERT: B 63 LEU cc_start: 0.7754 (tp) cc_final: 0.7361 (tp) REVERT: B 85 LEU cc_start: 0.7515 (mt) cc_final: 0.7045 (mt) REVERT: B 129 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.6621 (tpt) REVERT: C 80 ILE cc_start: 0.8413 (tp) cc_final: 0.8176 (tp) REVERT: C 219 MET cc_start: 0.6603 (ttt) cc_final: 0.6390 (ttm) REVERT: C 221 MET cc_start: 0.7799 (tpt) cc_final: 0.7352 (ttt) REVERT: D 54 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.4913 (ttm170) REVERT: a 16 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.5245 (ttp-110) REVERT: a 193 GLU cc_start: 0.7760 (tp30) cc_final: 0.7288 (tp30) REVERT: b 101 TRP cc_start: 0.7591 (t60) cc_final: 0.7320 (t60) outliers start: 30 outliers final: 23 residues processed: 167 average time/residue: 0.2325 time to fit residues: 52.4091 Evaluate side-chains 166 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain a residue 16 ARG Chi-restraints excluded: chain a residue 84 GLN Chi-restraints excluded: chain b residue 114 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 184 SER Chi-restraints excluded: chain b residue 206 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 0.0010 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS ** a 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 HIS a 190 ASN ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.184154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.154193 restraints weight = 9443.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.157379 restraints weight = 7687.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.159201 restraints weight = 6237.541| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9196 Z= 0.238 Angle : 0.656 10.256 12561 Z= 0.316 Chirality : 0.041 0.313 1483 Planarity : 0.005 0.061 1547 Dihedral : 9.260 85.041 1296 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.94 % Rotamer: Outliers : 3.34 % Allowed : 31.11 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.31 (0.26), residues: 1134 helix: 1.08 (0.20), residues: 727 sheet: -2.44 (0.69), residues: 50 loop : -1.12 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 179 HIS 0.002 0.001 HIS C 174 PHE 0.032 0.001 PHE A 24 TYR 0.009 0.001 TYR a 100 ARG 0.003 0.000 ARG a 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1852.71 seconds wall clock time: 34 minutes 27.19 seconds (2067.19 seconds total)