Starting phenix.real_space_refine on Sat Apr 6 18:39:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3s_41010/04_2024/8t3s_41010_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3s_41010/04_2024/8t3s_41010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3s_41010/04_2024/8t3s_41010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3s_41010/04_2024/8t3s_41010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3s_41010/04_2024/8t3s_41010_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3s_41010/04_2024/8t3s_41010_updated.pdb" } resolution = 3.07 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= 0.043 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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5600 2.51 5 N 1496 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 25": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 235": "OE1" <-> "OE2" Residue "R PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8769 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1797 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2063 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 14, 'TRANS': 243} Chain breaks: 3 Chain: "R" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 70 Unusual residues: {'BUA': 1, 'CLR': 1, 'PLM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.14, per 1000 atoms: 0.59 Number of scatterers: 8769 At special positions: 0 Unit cell: (84.252, 123.9, 119.77, 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 53 16.00 O 1620 8.00 N 1496 7.00 C 5600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 160 " - pdb=" SG CYS N 230 " distance=2.03 Simple disulfide: pdb=" SG CYS R 82 " - pdb=" SG CYS R 164 " distance=2.03 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: 3.43 Conformation dependent library (CDL) restraints added in 1.7 seconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 13 sheets defined 34.5% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.028A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 184 through 202 Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 5 through 37 Proline residue: R 23 - end of helix Processing helix chain 'R' and resid 43 through 60 Processing helix chain 'R' and resid 62 through 71 Processing helix chain 'R' and resid 79 through 112 removed outlier: 3.718A pdb=" N TYR R 90 " --> pdb=" O SER R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 120 Processing helix chain 'R' and resid 123 through 148 removed outlier: 3.559A pdb=" N ILE R 143 " --> pdb=" O GLY R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 186 removed outlier: 3.764A pdb=" N ASP R 174 " --> pdb=" O ASN R 171 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU R 177 " --> pdb=" O ASP R 174 " (cutoff:3.500A) Proline residue: R 178 - end of helix removed outlier: 3.651A pdb=" N LEU R 185 " --> pdb=" O GLU R 182 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL R 186 " --> pdb=" O LEU R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 208 Processing helix chain 'R' and resid 217 through 248 removed outlier: 3.596A pdb=" N VAL R 221 " --> pdb=" O ARG R 217 " (cutoff:3.500A) Proline residue: R 237 - end of helix removed outlier: 3.524A pdb=" N SER R 241 " --> pdb=" O PRO R 237 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS R 242 " --> pdb=" O TYR R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 273 removed outlier: 3.925A pdb=" N SER R 256 " --> pdb=" O TRP R 253 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL R 259 " --> pdb=" O SER R 256 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL R 260 " --> pdb=" O ILE R 257 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN R 265 " --> pdb=" O SER R 262 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP R 269 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Proline residue: R 270 - end of helix removed outlier: 3.599A pdb=" N PHE R 273 " --> pdb=" O PRO R 270 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 33 through 36 removed outlier: 6.658A pdb=" N ASN A 80 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU A 36 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N HIS A 82 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 38 through 40 removed outlier: 8.192A pdb=" N LEU A 39 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE A 107 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER A 138 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N PHE A 108 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE A 140 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL A 110 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE A 142 " --> pdb=" O VAL A 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.978A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.814A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.665A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 220 through 223 removed outlier: 4.186A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.465A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= I, first strand: chain 'B' and resid 45 through 50 removed outlier: 3.772A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 115 through 117 removed outlier: 5.469A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 141 through 143 Processing sheet with id= M, first strand: chain 'N' and resid 147 through 149 removed outlier: 6.593A pdb=" N LYS N 245 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU N 188 " --> pdb=" O LEU N 179 " (cutoff:3.500A) 389 hydrogen bonds defined for protein. 1077 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: 2.79 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1425 1.32 - 1.44: 2464 1.44 - 1.57: 4991 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8956 Sorted by residual: bond pdb=" CA SER B 74 " pdb=" CB SER B 74 " ideal model delta sigma weight residual 1.535 1.456 0.079 1.71e-02 3.42e+03 2.15e+01 bond pdb=" N GLN R 40 " pdb=" CA GLN R 40 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.66e+01 bond pdb=" CA SER B 72 " pdb=" CB SER B 72 " ideal model delta sigma weight residual 1.534 1.445 0.090 2.47e-02 1.64e+03 1.32e+01 bond pdb=" CA SER A 44 " pdb=" CB SER A 44 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.59e-02 3.96e+03 1.11e+01 bond pdb=" CA SER R 92 " pdb=" CB SER R 92 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.55e-02 4.16e+03 1.10e+01 ... (remaining 8951 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.83: 174 105.83 - 112.92: 4814 112.92 - 120.01: 3146 120.01 - 127.09: 3918 127.09 - 134.18: 96 Bond angle restraints: 12148 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 112.89 104.61 8.28 1.24e+00 6.50e-01 4.46e+01 angle pdb=" N ASP B 312 " pdb=" CA ASP B 312 " pdb=" CB ASP B 312 " ideal model delta sigma weight residual 114.17 107.50 6.67 1.14e+00 7.69e-01 3.42e+01 angle pdb=" N GLN B 75 " pdb=" CA GLN B 75 " pdb=" C GLN B 75 " ideal model delta sigma weight residual 113.21 106.62 6.59 1.15e+00 7.56e-01 3.28e+01 angle pdb=" N GLY B 77 " pdb=" CA GLY B 77 " pdb=" C GLY B 77 " ideal model delta sigma weight residual 115.72 108.97 6.75 1.51e+00 4.39e-01 2.00e+01 angle pdb=" N ALA R 13 " pdb=" CA ALA R 13 " pdb=" C ALA R 13 " ideal model delta sigma weight residual 111.07 106.29 4.78 1.07e+00 8.73e-01 1.99e+01 ... (remaining 12143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4701 17.98 - 35.95: 528 35.95 - 53.93: 117 53.93 - 71.90: 13 71.90 - 89.88: 3 Dihedral angle restraints: 5362 sinusoidal: 2120 harmonic: 3242 Sorted by residual: dihedral pdb=" C PRO R 252 " pdb=" N PRO R 252 " pdb=" CA PRO R 252 " pdb=" CB PRO R 252 " ideal model delta harmonic sigma weight residual -120.70 -110.61 -10.09 0 2.50e+00 1.60e-01 1.63e+01 dihedral pdb=" CA HIS B 311 " pdb=" C HIS B 311 " pdb=" N ASP B 312 " pdb=" CA ASP B 312 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " ideal model delta harmonic sigma weight residual 122.80 114.64 8.16 0 2.50e+00 1.60e-01 1.07e+01 ... (remaining 5359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1183 0.067 - 0.135: 168 0.135 - 0.202: 22 0.202 - 0.270: 4 0.270 - 0.337: 1 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CA VAL B 71 " pdb=" N VAL B 71 " pdb=" C VAL B 71 " pdb=" CB VAL B 71 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA LEU R 9 " pdb=" N LEU R 9 " pdb=" C LEU R 9 " pdb=" CB LEU R 9 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1375 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 86 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C SER R 86 " 0.059 2.00e-02 2.50e+03 pdb=" O SER R 86 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE R 87 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 62 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.77e+00 pdb=" N PRO R 63 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO R 63 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 63 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 13 " -0.012 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C ALA R 13 " 0.044 2.00e-02 2.50e+03 pdb=" O ALA R 13 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR R 14 " -0.015 2.00e-02 2.50e+03 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 527 2.73 - 3.27: 8760 3.27 - 3.81: 14890 3.81 - 4.36: 17963 4.36 - 4.90: 31456 Nonbonded interactions: 73596 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.185 2.440 nonbonded pdb=" O ALA R 133 " pdb=" OG SER R 137 " model vdw 2.196 2.440 nonbonded pdb=" O TYR R 238 " pdb=" OG SER R 241 " model vdw 2.227 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.253 2.440 ... (remaining 73591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 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: 0.910 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: 4.210 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.300 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 : 0.005 0.090 8956 Z= 0.341 Angle : 0.748 8.283 12148 Z= 0.498 Chirality : 0.051 0.337 1378 Planarity : 0.005 0.065 1536 Dihedral : 15.215 89.881 3261 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.53 % Allowed : 21.66 % Favored : 77.80 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.56 % 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: 0.78 (0.26), residues: 1099 helix: 1.51 (0.26), residues: 381 sheet: 0.16 (0.32), residues: 272 loop : 0.01 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 254 HIS 0.004 0.001 HIS A 214 PHE 0.028 0.002 PHE N 240 TYR 0.043 0.002 TYR R 14 ARG 0.016 0.001 ARG R 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 1.021 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 139 average time/residue: 0.2342 time to fit residues: 43.9023 Evaluate side-chains 131 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 268 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.0060 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN R 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8956 Z= 0.180 Angle : 0.502 8.110 12148 Z= 0.266 Chirality : 0.041 0.139 1378 Planarity : 0.004 0.063 1536 Dihedral : 4.577 59.134 1314 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.56 % Allowed : 20.17 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1099 helix: 1.82 (0.26), residues: 382 sheet: 0.17 (0.32), residues: 276 loop : 0.29 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.024 0.001 PHE R 18 TYR 0.019 0.001 TYR R 14 ARG 0.003 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.016 Fit side-chains REVERT: A 199 ASP cc_start: 0.8168 (m-30) cc_final: 0.7740 (m-30) REVERT: B 59 TYR cc_start: 0.8211 (m-80) cc_final: 0.7537 (m-80) REVERT: N 87 ARG cc_start: 0.7675 (ptp-170) cc_final: 0.7403 (ptp-170) REVERT: R 243 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8451 (mp) outliers start: 24 outliers final: 16 residues processed: 152 average time/residue: 0.2212 time to fit residues: 46.2282 Evaluate side-chains 147 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 0.0980 chunk 99 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8956 Z= 0.258 Angle : 0.523 9.174 12148 Z= 0.271 Chirality : 0.042 0.152 1378 Planarity : 0.004 0.053 1536 Dihedral : 4.456 32.218 1312 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.84 % Allowed : 19.96 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.06 (0.25), residues: 1099 helix: 1.73 (0.26), residues: 387 sheet: 0.10 (0.31), residues: 265 loop : 0.32 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 254 HIS 0.004 0.001 HIS B 311 PHE 0.024 0.002 PHE N 68 TYR 0.017 0.002 TYR R 165 ARG 0.003 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 0.941 Fit side-chains REVERT: A 122 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8400 (mp) REVERT: A 199 ASP cc_start: 0.8236 (m-30) cc_final: 0.7798 (m-30) REVERT: N 161 ARG cc_start: 0.7631 (ttp-110) cc_final: 0.7308 (mtp85) REVERT: R 106 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7348 (tm-30) outliers start: 36 outliers final: 23 residues processed: 156 average time/residue: 0.2304 time to fit residues: 49.0239 Evaluate side-chains 147 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8956 Z= 0.176 Angle : 0.485 7.943 12148 Z= 0.251 Chirality : 0.041 0.168 1378 Planarity : 0.003 0.049 1536 Dihedral : 4.279 31.737 1312 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.31 % Allowed : 21.13 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1099 helix: 1.94 (0.26), residues: 381 sheet: 0.06 (0.30), residues: 279 loop : 0.26 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 254 HIS 0.004 0.001 HIS B 311 PHE 0.016 0.001 PHE R 18 TYR 0.016 0.001 TYR R 165 ARG 0.005 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.009 Fit side-chains REVERT: A 73 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7781 (mtpt) REVERT: A 194 ARG cc_start: 0.7592 (ttt-90) cc_final: 0.7362 (ttt-90) REVERT: A 199 ASP cc_start: 0.8191 (m-30) cc_final: 0.7764 (m-30) REVERT: B 338 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8525 (mm) REVERT: N 161 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7350 (mtp85) REVERT: R 187 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7868 (mp) outliers start: 31 outliers final: 22 residues processed: 144 average time/residue: 0.2354 time to fit residues: 46.1421 Evaluate side-chains 146 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0570 chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8956 Z= 0.255 Angle : 0.518 8.740 12148 Z= 0.268 Chirality : 0.042 0.176 1378 Planarity : 0.004 0.046 1536 Dihedral : 4.544 32.761 1312 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.38 % Allowed : 20.17 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.13 (0.25), residues: 1099 helix: 1.93 (0.26), residues: 385 sheet: -0.02 (0.31), residues: 266 loop : 0.35 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 254 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.002 PHE R 18 TYR 0.015 0.002 TYR R 165 ARG 0.005 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 130 time to evaluate : 0.978 Fit side-chains REVERT: A 122 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8458 (mp) REVERT: A 199 ASP cc_start: 0.8149 (m-30) cc_final: 0.7681 (m-30) REVERT: B 338 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8660 (mm) REVERT: N 87 ARG cc_start: 0.7857 (ptp-170) cc_final: 0.7610 (ptp-170) REVERT: N 161 ARG cc_start: 0.7686 (ttp-110) cc_final: 0.7346 (mtp85) REVERT: R 106 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7417 (tm-30) REVERT: R 187 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7833 (mp) outliers start: 41 outliers final: 30 residues processed: 158 average time/residue: 0.2144 time to fit residues: 46.9962 Evaluate side-chains 158 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 257 ILE Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 62 optimal weight: 0.4980 chunk 26 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8956 Z= 0.145 Angle : 0.471 8.122 12148 Z= 0.243 Chirality : 0.040 0.174 1378 Planarity : 0.003 0.045 1536 Dihedral : 4.200 29.919 1312 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.09 % Allowed : 21.56 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1099 helix: 2.13 (0.26), residues: 381 sheet: 0.07 (0.31), residues: 264 loop : 0.30 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 254 HIS 0.003 0.001 HIS B 311 PHE 0.023 0.001 PHE R 18 TYR 0.015 0.001 TYR R 165 ARG 0.004 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 0.963 Fit side-chains REVERT: A 122 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8434 (mp) REVERT: A 199 ASP cc_start: 0.8099 (m-30) cc_final: 0.7594 (m-30) REVERT: B 338 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8521 (mm) REVERT: N 161 ARG cc_start: 0.7638 (ttp-110) cc_final: 0.7349 (mtp85) REVERT: R 106 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: R 187 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7923 (mp) outliers start: 29 outliers final: 19 residues processed: 146 average time/residue: 0.2337 time to fit residues: 46.8111 Evaluate side-chains 144 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 257 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.0570 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 0.0470 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8956 Z= 0.132 Angle : 0.467 8.149 12148 Z= 0.242 Chirality : 0.040 0.165 1378 Planarity : 0.003 0.045 1536 Dihedral : 3.951 27.321 1312 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.52 % Allowed : 21.66 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.36 (0.26), residues: 1099 helix: 2.27 (0.26), residues: 382 sheet: 0.12 (0.31), residues: 262 loop : 0.32 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 254 HIS 0.003 0.001 HIS B 311 PHE 0.019 0.001 PHE R 18 TYR 0.014 0.001 TYR R 165 ARG 0.003 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 127 time to evaluate : 1.012 Fit side-chains REVERT: A 122 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8394 (mp) REVERT: A 132 ARG cc_start: 0.8163 (mtm180) cc_final: 0.7708 (ptt180) REVERT: B 338 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8499 (mm) REVERT: N 87 ARG cc_start: 0.7738 (ptp-170) cc_final: 0.7407 (ptp-170) REVERT: N 161 ARG cc_start: 0.7565 (ttp-110) cc_final: 0.7289 (mtp85) REVERT: R 106 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7448 (tm-30) REVERT: R 187 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7849 (mp) outliers start: 33 outliers final: 20 residues processed: 152 average time/residue: 0.2221 time to fit residues: 46.3375 Evaluate side-chains 147 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 257 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 67 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8956 Z= 0.194 Angle : 0.490 7.945 12148 Z= 0.252 Chirality : 0.041 0.182 1378 Planarity : 0.003 0.045 1536 Dihedral : 4.094 27.482 1312 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.52 % Allowed : 21.66 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1099 helix: 2.12 (0.26), residues: 388 sheet: 0.17 (0.31), residues: 260 loop : 0.27 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 254 HIS 0.003 0.001 HIS B 91 PHE 0.022 0.001 PHE R 18 TYR 0.014 0.001 TYR R 165 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 125 time to evaluate : 1.032 Fit side-chains REVERT: A 122 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8373 (mp) REVERT: A 132 ARG cc_start: 0.8180 (mtm180) cc_final: 0.7712 (ptt180) REVERT: B 338 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8505 (mm) REVERT: N 161 ARG cc_start: 0.7580 (ttp-110) cc_final: 0.7309 (mtp85) REVERT: R 12 MET cc_start: 0.7101 (ptm) cc_final: 0.6897 (ptm) REVERT: R 106 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: R 187 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7900 (mp) outliers start: 33 outliers final: 26 residues processed: 149 average time/residue: 0.2304 time to fit residues: 46.7600 Evaluate side-chains 154 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 257 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 59 optimal weight: 0.0070 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 0.0970 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 247 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8956 Z= 0.131 Angle : 0.472 8.506 12148 Z= 0.244 Chirality : 0.040 0.181 1378 Planarity : 0.003 0.045 1536 Dihedral : 3.903 26.901 1312 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.20 % Allowed : 21.77 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.36 (0.26), residues: 1099 helix: 2.31 (0.26), residues: 383 sheet: 0.17 (0.31), residues: 272 loop : 0.24 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS A 82 PHE 0.025 0.001 PHE R 18 TYR 0.013 0.001 TYR R 165 ARG 0.004 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 0.938 Fit side-chains REVERT: A 122 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8344 (mp) REVERT: A 132 ARG cc_start: 0.8142 (mtm180) cc_final: 0.7735 (ptt180) REVERT: B 237 ASN cc_start: 0.8760 (p0) cc_final: 0.8463 (p0) REVERT: B 338 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8443 (mm) REVERT: N 87 ARG cc_start: 0.7743 (ptp-170) cc_final: 0.7396 (ptp-170) REVERT: N 161 ARG cc_start: 0.7551 (ttp-110) cc_final: 0.7274 (mtp85) REVERT: R 12 MET cc_start: 0.7134 (ptm) cc_final: 0.6913 (ptm) REVERT: R 106 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: R 187 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7957 (mp) outliers start: 30 outliers final: 26 residues processed: 151 average time/residue: 0.2209 time to fit residues: 45.9667 Evaluate side-chains 155 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 257 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8956 Z= 0.174 Angle : 0.488 8.375 12148 Z= 0.253 Chirality : 0.041 0.171 1378 Planarity : 0.003 0.046 1536 Dihedral : 3.985 27.092 1312 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.31 % Allowed : 21.77 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 1099 helix: 2.20 (0.26), residues: 389 sheet: 0.20 (0.31), residues: 260 loop : 0.25 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 254 HIS 0.003 0.001 HIS B 91 PHE 0.023 0.001 PHE R 18 TYR 0.014 0.001 TYR B 59 ARG 0.003 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.014 Fit side-chains REVERT: A 122 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8360 (mp) REVERT: A 132 ARG cc_start: 0.8164 (mtm180) cc_final: 0.7748 (ptt180) REVERT: B 237 ASN cc_start: 0.8776 (p0) cc_final: 0.8528 (p0) REVERT: B 338 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8497 (mm) REVERT: N 87 ARG cc_start: 0.7752 (ptp-170) cc_final: 0.7444 (ptp-170) REVERT: N 161 ARG cc_start: 0.7579 (ttp-110) cc_final: 0.7295 (mtp85) REVERT: R 12 MET cc_start: 0.7113 (ptm) cc_final: 0.6905 (ptm) REVERT: R 106 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: R 187 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7888 (mp) outliers start: 31 outliers final: 26 residues processed: 149 average time/residue: 0.2234 time to fit residues: 45.4786 Evaluate side-chains 154 residues out of total 956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain R residue 106 GLU Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 ASN Chi-restraints excluded: chain R residue 257 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.157464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112188 restraints weight = 9747.219| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.26 r_work: 0.3029 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8956 Z= 0.362 Angle : 0.567 9.161 12148 Z= 0.295 Chirality : 0.044 0.165 1378 Planarity : 0.004 0.046 1536 Dihedral : 4.718 40.852 1312 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.31 % Allowed : 21.99 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.06 (0.26), residues: 1099 helix: 1.92 (0.26), residues: 395 sheet: -0.03 (0.32), residues: 254 loop : 0.17 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 254 HIS 0.005 0.001 HIS B 91 PHE 0.025 0.002 PHE R 18 TYR 0.014 0.002 TYR B 59 ARG 0.003 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2313.02 seconds wall clock time: 42 minutes 58.61 seconds (2578.61 seconds total)