Starting phenix.real_space_refine on Mon Mar 11 18:09:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk2_33241/03_2024/7xk2_33241_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk2_33241/03_2024/7xk2_33241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk2_33241/03_2024/7xk2_33241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk2_33241/03_2024/7xk2_33241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk2_33241/03_2024/7xk2_33241_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk2_33241/03_2024/7xk2_33241_updated.pdb" } resolution = 3.1 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= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5594 2.51 5 N 1509 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 186": "OE1" <-> "OE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "R PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 190": "OE1" <-> "OE2" Residue "R ASP 273": "OD1" <-> "OD2" Residue "R PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 137": "OD1" <-> "OD2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8791 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1798 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2596 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2229 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 274} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "S" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1711 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 429 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'FI7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.45, per 1000 atoms: 0.62 Number of scatterers: 8791 At special positions: 0 Unit cell: (87.36, 116.48, 132.08, 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 66 16.00 O 1622 8.00 N 1509 7.00 C 5594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " 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: 3.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 13 sheets defined 31.4% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 272 through 280 removed outlier: 4.655A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 4 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 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'R' and resid 26 through 52 Proline residue: R 31 - end of helix removed outlier: 3.966A pdb=" N LEU R 43 " --> pdb=" O ILE R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 79 removed outlier: 3.894A pdb=" N PHE R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 85 No H-bonds generated for 'chain 'R' and resid 82 through 85' Processing helix chain 'R' and resid 98 through 129 removed outlier: 4.038A pdb=" N LEU R 104 " --> pdb=" O CYS R 100 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE R 105 " --> pdb=" O ARG R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 157 Processing helix chain 'R' and resid 160 through 164 removed outlier: 3.989A pdb=" N LYS R 164 " --> pdb=" O HIS R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 217 removed outlier: 3.808A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 3.589A pdb=" N LEU R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA R 209 " --> pdb=" O LEU R 205 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG R 210 " --> pdb=" O PHE R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 260 removed outlier: 3.843A pdb=" N ILE R 233 " --> pdb=" O ALA R 229 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 270 through 289 removed outlier: 4.213A pdb=" N ASP R 273 " --> pdb=" O ARG R 270 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU R 274 " --> pdb=" O SER R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 291 through 293 No H-bonds generated for 'chain 'R' and resid 291 through 293' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 75 through 77 No H-bonds generated for 'chain 'S' and resid 75 through 77' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing sheet with id= A, first strand: chain 'A' and resid 220 through 224 removed outlier: 6.772A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.759A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.007A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.739A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.540A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.836A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.623A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.849A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 18 through 23 Processing sheet with id= J, first strand: chain 'S' and resid 33 through 35 Processing sheet with id= K, first strand: chain 'S' and resid 49 through 51 Processing sheet with id= L, first strand: chain 'S' and resid 156 through 160 Processing sheet with id= M, first strand: chain 'S' and resid 226 through 231 removed outlier: 5.813A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 921 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: 2.54 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2528 1.34 - 1.46: 1693 1.46 - 1.57: 4662 1.57 - 1.69: 2 1.69 - 1.81: 96 Bond restraints: 8981 Sorted by residual: bond pdb=" C02 FI7 R 401 " pdb=" C17 FI7 R 401 " ideal model delta sigma weight residual 1.545 1.627 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C17 FI7 R 401 " pdb=" N19 FI7 R 401 " ideal model delta sigma weight residual 1.348 1.414 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C07 FI7 R 401 " pdb=" N15 FI7 R 401 " ideal model delta sigma weight residual 1.300 1.365 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C02 FI7 R 401 " pdb=" C04 FI7 R 401 " ideal model delta sigma weight residual 1.546 1.606 -0.060 2.00e-02 2.50e+03 9.14e+00 bond pdb=" C05 FI7 R 401 " pdb=" O16 FI7 R 401 " ideal model delta sigma weight residual 1.330 1.390 -0.060 2.00e-02 2.50e+03 8.96e+00 ... (remaining 8976 not shown) Histogram of bond angle deviations from ideal: 93.56 - 101.68: 29 101.68 - 109.80: 1220 109.80 - 117.92: 5379 117.92 - 126.05: 5361 126.05 - 134.17: 172 Bond angle restraints: 12161 Sorted by residual: angle pdb=" CA GLN A 52 " pdb=" CB GLN A 52 " pdb=" CG GLN A 52 " ideal model delta sigma weight residual 114.10 124.36 -10.26 2.00e+00 2.50e-01 2.63e+01 angle pdb=" C ALA R 174 " pdb=" N ASN R 175 " pdb=" CA ASN R 175 " ideal model delta sigma weight residual 122.46 129.13 -6.67 1.41e+00 5.03e-01 2.23e+01 angle pdb=" CA LYS C 20 " pdb=" CB LYS C 20 " pdb=" CG LYS C 20 " ideal model delta sigma weight residual 114.10 123.43 -9.33 2.00e+00 2.50e-01 2.18e+01 angle pdb=" C THR R 283 " pdb=" N TYR R 284 " pdb=" CA TYR R 284 " ideal model delta sigma weight residual 121.58 112.72 8.86 1.95e+00 2.63e-01 2.07e+01 angle pdb=" CA TYR R 284 " pdb=" CB TYR R 284 " pdb=" CG TYR R 284 " ideal model delta sigma weight residual 113.90 121.60 -7.70 1.80e+00 3.09e-01 1.83e+01 ... (remaining 12156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4590 17.63 - 35.25: 579 35.25 - 52.88: 133 52.88 - 70.51: 20 70.51 - 88.14: 7 Dihedral angle restraints: 5329 sinusoidal: 2063 harmonic: 3266 Sorted by residual: dihedral pdb=" CB CYS R 19 " pdb=" SG CYS R 19 " pdb=" SG CYS R 266 " pdb=" CB CYS R 266 " ideal model delta sinusoidal sigma weight residual 93.00 160.11 -67.11 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CB CYS R 18 " pdb=" SG CYS R 18 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual -86.00 -35.39 -50.61 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CA TYR S 94 " pdb=" C TYR S 94 " pdb=" N TYR S 95 " pdb=" CA TYR S 95 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 5326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1255 0.100 - 0.199: 99 0.199 - 0.298: 8 0.298 - 0.398: 1 0.398 - 0.497: 1 Chirality restraints: 1364 Sorted by residual: chirality pdb=" CB ILE R 238 " pdb=" CA ILE R 238 " pdb=" CG1 ILE R 238 " pdb=" CG2 ILE R 238 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CG LEU R 80 " pdb=" CB LEU R 80 " pdb=" CD1 LEU R 80 " pdb=" CD2 LEU R 80 " both_signs ideal model delta sigma weight residual False -2.59 -2.91 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA TYR R 284 " pdb=" N TYR R 284 " pdb=" C TYR R 284 " pdb=" CB TYR R 284 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1361 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 265 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C ILE A 265 " -0.049 2.00e-02 2.50e+03 pdb=" O ILE A 265 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 266 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 134 " 0.191 9.50e-02 1.11e+02 8.64e-02 5.90e+00 pdb=" NE ARG B 134 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 134 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG B 134 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 134 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 197 " -0.181 9.50e-02 1.11e+02 8.18e-02 5.17e+00 pdb=" NE ARG B 197 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 197 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 197 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 197 " -0.001 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1917 2.78 - 3.31: 7760 3.31 - 3.84: 14885 3.84 - 4.37: 17158 4.37 - 4.90: 29664 Nonbonded interactions: 71384 Sorted by model distance: nonbonded pdb=" O ILE R 278 " pdb=" OG SER R 281 " model vdw 2.251 2.440 nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.291 2.440 nonbonded pdb=" OE1 GLN S 142 " pdb=" OG1 THR S 243 " model vdw 2.297 2.440 nonbonded pdb=" OG SER S 206 " pdb=" O THR S 213 " model vdw 2.313 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.329 2.440 ... (remaining 71379 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: 3.960 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.820 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 0.082 8981 Z= 0.325 Angle : 1.022 13.801 12161 Z= 0.515 Chirality : 0.056 0.497 1364 Planarity : 0.007 0.086 1542 Dihedral : 16.480 88.136 3210 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.32 % Allowed : 22.03 % Favored : 77.65 % 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: -2.41 (0.23), residues: 1114 helix: -1.04 (0.25), residues: 355 sheet: -1.11 (0.30), residues: 265 loop : -2.24 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS R 223 PHE 0.036 0.002 PHE A 334 TYR 0.035 0.002 TYR S 235 ARG 0.021 0.001 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: B 301 LYS cc_start: 0.7031 (ptmm) cc_final: 0.6631 (pttt) REVERT: S 80 PHE cc_start: 0.8645 (m-80) cc_final: 0.8348 (m-80) REVERT: C 18 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7645 (tp-100) outliers start: 3 outliers final: 2 residues processed: 172 average time/residue: 0.2268 time to fit residues: 52.4272 Evaluate side-chains 169 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 280 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.1980 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 110 ASN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8981 Z= 0.174 Angle : 0.580 8.266 12161 Z= 0.296 Chirality : 0.041 0.171 1364 Planarity : 0.004 0.044 1542 Dihedral : 5.513 51.436 1247 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.67 % Allowed : 22.67 % Favored : 74.65 % 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: -1.67 (0.24), residues: 1114 helix: 0.26 (0.27), residues: 352 sheet: -1.24 (0.29), residues: 268 loop : -2.02 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS R 223 PHE 0.013 0.001 PHE S 27 TYR 0.027 0.001 TYR S 235 ARG 0.006 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 0.990 Fit side-chains REVERT: A 336 PHE cc_start: 0.8533 (t80) cc_final: 0.8319 (t80) REVERT: B 114 CYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7936 (p) REVERT: S 43 LYS cc_start: 0.7820 (mppt) cc_final: 0.7353 (mmtm) REVERT: S 180 ARG cc_start: 0.8297 (mtm-85) cc_final: 0.8021 (mtt-85) outliers start: 25 outliers final: 17 residues processed: 191 average time/residue: 0.2297 time to fit residues: 58.8527 Evaluate side-chains 183 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 175 TYR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8981 Z= 0.271 Angle : 0.616 11.681 12161 Z= 0.313 Chirality : 0.042 0.239 1364 Planarity : 0.004 0.040 1542 Dihedral : 5.651 59.151 1247 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.06 % Allowed : 23.10 % Favored : 72.83 % 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: -1.46 (0.24), residues: 1114 helix: 0.58 (0.28), residues: 361 sheet: -1.29 (0.29), residues: 266 loop : -1.96 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.018 0.001 PHE S 27 TYR 0.034 0.002 TYR S 235 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 171 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: B 87 THR cc_start: 0.8647 (m) cc_final: 0.8443 (p) REVERT: B 114 CYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7956 (p) REVERT: B 155 ASN cc_start: 0.7606 (t0) cc_final: 0.7270 (t0) REVERT: B 214 ARG cc_start: 0.8032 (mpp80) cc_final: 0.7784 (mpp80) REVERT: R 194 LEU cc_start: 0.8239 (mm) cc_final: 0.7933 (tp) REVERT: R 227 LYS cc_start: 0.8192 (mmmm) cc_final: 0.7750 (mppt) REVERT: S 18 ARG cc_start: 0.7420 (tpp-160) cc_final: 0.7000 (tpp-160) REVERT: S 235 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.6646 (t80) outliers start: 38 outliers final: 23 residues processed: 196 average time/residue: 0.2366 time to fit residues: 61.9884 Evaluate side-chains 190 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 175 TYR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 28 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 269 ASN B 237 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8981 Z= 0.186 Angle : 0.570 10.105 12161 Z= 0.288 Chirality : 0.041 0.237 1364 Planarity : 0.004 0.038 1542 Dihedral : 5.320 54.060 1247 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.24 % Allowed : 23.74 % Favored : 71.02 % 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: -1.20 (0.25), residues: 1114 helix: 0.90 (0.28), residues: 354 sheet: -1.24 (0.29), residues: 266 loop : -1.79 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS A 188 PHE 0.013 0.001 PHE S 27 TYR 0.028 0.001 TYR S 235 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 173 time to evaluate : 1.069 Fit side-chains REVERT: A 207 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7193 (tt0) REVERT: A 266 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8792 (tp) REVERT: B 114 CYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7972 (p) REVERT: B 214 ARG cc_start: 0.8015 (mpp80) cc_final: 0.7773 (mpp80) REVERT: B 229 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7637 (pt) REVERT: B 234 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8917 (m-80) REVERT: R 110 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7935 (m110) REVERT: R 194 LEU cc_start: 0.8111 (mm) cc_final: 0.7707 (tp) REVERT: R 219 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6769 (tp40) REVERT: R 227 LYS cc_start: 0.8150 (mmmm) cc_final: 0.7724 (mppt) REVERT: R 258 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7697 (mp) REVERT: R 282 PHE cc_start: 0.8409 (m-80) cc_final: 0.8196 (m-80) REVERT: S 235 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6541 (t80) outliers start: 49 outliers final: 25 residues processed: 206 average time/residue: 0.2353 time to fit residues: 65.8629 Evaluate side-chains 199 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 161 HIS Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 0.0980 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8981 Z= 0.210 Angle : 0.585 9.575 12161 Z= 0.294 Chirality : 0.042 0.254 1364 Planarity : 0.004 0.042 1542 Dihedral : 5.215 48.076 1247 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.78 % Allowed : 23.85 % Favored : 70.37 % 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: -1.09 (0.25), residues: 1114 helix: 1.07 (0.29), residues: 354 sheet: -1.20 (0.30), residues: 267 loop : -1.77 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS R 223 PHE 0.014 0.001 PHE R 117 TYR 0.029 0.001 TYR S 235 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 175 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7196 (tt0) REVERT: A 266 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8800 (tp) REVERT: B 114 CYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7964 (p) REVERT: B 155 ASN cc_start: 0.7580 (t0) cc_final: 0.7328 (t0) REVERT: B 214 ARG cc_start: 0.8018 (mpp80) cc_final: 0.7795 (mpp80) REVERT: B 229 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7672 (pt) REVERT: B 234 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8896 (m-80) REVERT: R 110 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7942 (m110) REVERT: R 194 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7657 (tp) REVERT: R 219 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6816 (tp40) REVERT: R 258 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7721 (mp) REVERT: S 43 LYS cc_start: 0.8285 (mmmt) cc_final: 0.7956 (mmmt) REVERT: S 180 ARG cc_start: 0.8312 (mtm-85) cc_final: 0.7867 (mtt90) REVERT: S 235 TYR cc_start: 0.7361 (OUTLIER) cc_final: 0.6488 (t80) outliers start: 54 outliers final: 29 residues processed: 216 average time/residue: 0.2235 time to fit residues: 64.9940 Evaluate side-chains 210 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 171 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 161 HIS Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 194 ASN Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 189 HIS ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8981 Z= 0.271 Angle : 0.635 14.214 12161 Z= 0.316 Chirality : 0.043 0.250 1364 Planarity : 0.004 0.047 1542 Dihedral : 5.212 34.033 1245 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.35 % Allowed : 24.17 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.25), residues: 1114 helix: 1.06 (0.29), residues: 353 sheet: -1.19 (0.30), residues: 268 loop : -1.79 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.017 0.001 PHE S 27 TYR 0.034 0.002 TYR S 235 ARG 0.011 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 175 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: A 266 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8797 (tp) REVERT: B 114 CYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7913 (p) REVERT: B 155 ASN cc_start: 0.7625 (t0) cc_final: 0.7366 (t0) REVERT: B 204 CYS cc_start: 0.8049 (m) cc_final: 0.7358 (t) REVERT: B 214 ARG cc_start: 0.8049 (mpp80) cc_final: 0.7837 (mpp80) REVERT: B 234 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8923 (m-80) REVERT: R 110 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.8031 (m110) REVERT: R 194 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7650 (tp) REVERT: R 227 LYS cc_start: 0.8250 (mmmm) cc_final: 0.7748 (mppt) REVERT: R 258 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7666 (mp) REVERT: R 282 PHE cc_start: 0.8423 (m-80) cc_final: 0.8193 (m-80) REVERT: S 180 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7754 (mtt90) REVERT: S 235 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6372 (t80) outliers start: 50 outliers final: 30 residues processed: 209 average time/residue: 0.2315 time to fit residues: 64.8647 Evaluate side-chains 208 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 170 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 277 PHE Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8981 Z= 0.249 Angle : 0.609 13.327 12161 Z= 0.305 Chirality : 0.042 0.263 1364 Planarity : 0.004 0.048 1542 Dihedral : 5.214 36.913 1245 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.60 % Allowed : 25.67 % Favored : 69.73 % 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: -1.07 (0.25), residues: 1114 helix: 1.10 (0.28), residues: 354 sheet: -1.23 (0.30), residues: 270 loop : -1.75 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.016 0.001 PHE R 117 TYR 0.032 0.001 TYR S 235 ARG 0.012 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 174 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7235 (tt0) REVERT: A 266 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8800 (tp) REVERT: A 349 LYS cc_start: 0.8046 (mptt) cc_final: 0.7829 (mptp) REVERT: B 114 CYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7954 (p) REVERT: B 204 CYS cc_start: 0.8014 (m) cc_final: 0.7349 (t) REVERT: B 214 ARG cc_start: 0.8070 (mpp80) cc_final: 0.7832 (mpp80) REVERT: B 234 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8939 (m-80) REVERT: R 110 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.8014 (m110) REVERT: R 194 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7609 (tp) REVERT: R 227 LYS cc_start: 0.8247 (mmmm) cc_final: 0.7755 (mppt) REVERT: R 282 PHE cc_start: 0.8419 (m-80) cc_final: 0.8103 (m-80) REVERT: S 180 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.7878 (mtt90) REVERT: S 235 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6305 (t80) outliers start: 43 outliers final: 31 residues processed: 204 average time/residue: 0.2367 time to fit residues: 64.0951 Evaluate side-chains 205 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 7.9990 chunk 31 optimal weight: 0.0010 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8981 Z= 0.247 Angle : 0.611 12.983 12161 Z= 0.307 Chirality : 0.042 0.269 1364 Planarity : 0.004 0.052 1542 Dihedral : 5.213 36.647 1245 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 5.13 % Allowed : 24.81 % Favored : 70.05 % 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: -1.09 (0.25), residues: 1114 helix: 1.20 (0.29), residues: 347 sheet: -1.22 (0.30), residues: 270 loop : -1.83 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.019 0.001 PHE R 117 TYR 0.032 0.001 TYR S 235 ARG 0.013 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 173 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7234 (tt0) REVERT: A 266 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8812 (tp) REVERT: A 349 LYS cc_start: 0.8042 (mptt) cc_final: 0.7773 (mptp) REVERT: B 114 CYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7957 (p) REVERT: B 172 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7776 (pm20) REVERT: B 204 CYS cc_start: 0.7958 (m) cc_final: 0.7323 (t) REVERT: B 214 ARG cc_start: 0.8068 (mpp80) cc_final: 0.7838 (mpp80) REVERT: B 234 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8944 (m-80) REVERT: R 110 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.8002 (m110) REVERT: R 194 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7579 (tp) REVERT: R 282 PHE cc_start: 0.8374 (m-80) cc_final: 0.8134 (m-80) REVERT: S 235 TYR cc_start: 0.7199 (OUTLIER) cc_final: 0.6260 (t80) outliers start: 48 outliers final: 36 residues processed: 206 average time/residue: 0.2336 time to fit residues: 64.0198 Evaluate side-chains 213 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 169 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 161 HIS Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.3980 chunk 101 optimal weight: 0.4980 chunk 59 optimal weight: 7.9990 chunk 43 optimal weight: 0.3980 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 64 optimal weight: 4.9990 chunk 104 optimal weight: 0.4980 chunk 63 optimal weight: 6.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8981 Z= 0.170 Angle : 0.599 12.705 12161 Z= 0.296 Chirality : 0.042 0.278 1364 Planarity : 0.004 0.055 1542 Dihedral : 4.997 36.426 1245 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.74 % Allowed : 26.42 % Favored : 69.84 % 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: -0.95 (0.25), residues: 1114 helix: 1.35 (0.29), residues: 347 sheet: -1.10 (0.30), residues: 270 loop : -1.80 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS A 188 PHE 0.019 0.001 PHE R 117 TYR 0.027 0.001 TYR S 235 ARG 0.014 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: A 266 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8767 (tp) REVERT: B 172 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: B 204 CYS cc_start: 0.7790 (m) cc_final: 0.7239 (t) REVERT: B 214 ARG cc_start: 0.8054 (mpp80) cc_final: 0.7815 (mpp80) REVERT: R 110 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7993 (m110) REVERT: R 194 LEU cc_start: 0.8000 (mm) cc_final: 0.7544 (tp) REVERT: R 282 PHE cc_start: 0.8380 (m-80) cc_final: 0.8143 (m-80) REVERT: S 235 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6295 (t80) outliers start: 35 outliers final: 27 residues processed: 194 average time/residue: 0.2270 time to fit residues: 59.0391 Evaluate side-chains 198 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 166 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 0.2980 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8981 Z= 0.261 Angle : 0.637 12.664 12161 Z= 0.317 Chirality : 0.043 0.275 1364 Planarity : 0.004 0.060 1542 Dihedral : 5.162 36.417 1245 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.96 % Allowed : 25.88 % Favored : 70.16 % 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: -1.00 (0.25), residues: 1114 helix: 1.29 (0.29), residues: 347 sheet: -1.14 (0.30), residues: 270 loop : -1.81 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.020 0.001 PHE R 117 TYR 0.033 0.002 TYR S 235 ARG 0.014 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 169 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: A 266 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8822 (tp) REVERT: B 114 CYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7957 (p) REVERT: B 204 CYS cc_start: 0.7981 (m) cc_final: 0.7333 (t) REVERT: B 214 ARG cc_start: 0.8070 (mpp80) cc_final: 0.7838 (mpp80) REVERT: R 110 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7950 (m110) REVERT: R 194 LEU cc_start: 0.8014 (mm) cc_final: 0.7549 (tp) REVERT: R 227 LYS cc_start: 0.8246 (mmmm) cc_final: 0.7743 (mppt) REVERT: R 282 PHE cc_start: 0.8380 (m-80) cc_final: 0.8133 (m-80) REVERT: S 235 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.6095 (t80) outliers start: 37 outliers final: 29 residues processed: 195 average time/residue: 0.2384 time to fit residues: 61.5927 Evaluate side-chains 201 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 185 THR Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 284 TYR Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 0.0570 chunk 4 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.187659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122658 restraints weight = 10209.498| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.67 r_work: 0.3164 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8981 Z= 0.201 Angle : 0.614 12.625 12161 Z= 0.304 Chirality : 0.042 0.273 1364 Planarity : 0.004 0.059 1542 Dihedral : 5.078 35.720 1245 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.96 % Allowed : 26.10 % Favored : 69.95 % 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: -0.92 (0.25), residues: 1114 helix: 1.35 (0.29), residues: 347 sheet: -1.07 (0.30), residues: 271 loop : -1.78 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 PHE 0.019 0.001 PHE R 117 TYR 0.029 0.001 TYR S 235 ARG 0.014 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2370.87 seconds wall clock time: 43 minutes 42.66 seconds (2622.66 seconds total)