Starting phenix.real_space_refine on Mon Mar 11 15:42:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuz_32132/03_2024/7vuz_32132_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuz_32132/03_2024/7vuz_32132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuz_32132/03_2024/7vuz_32132.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuz_32132/03_2024/7vuz_32132.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuz_32132/03_2024/7vuz_32132_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vuz_32132/03_2024/7vuz_32132_updated.pdb" } resolution = 2.89 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= 0.004 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 64 5.16 5 C 5493 2.51 5 N 1439 2.21 5 O 1588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R ARG 141": "NH1" <-> "NH2" Residue "R ARG 143": "NH1" <-> "NH2" Residue "R PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 208": "NH1" <-> "NH2" Residue "R ARG 220": "NH1" <-> "NH2" Residue "R PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 252": "OD1" <-> "OD2" Residue "R ASP 254": "OD1" <-> "OD2" Residue "R TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ASP 26": "OD1" <-> "OD2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 73": "OD1" <-> "OD2" Residue "S TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 148": "NH1" <-> "NH2" Residue "S TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 222": "OE1" <-> "OE2" 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: 8584 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1995 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1750 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2598 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 427 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1786 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.99, per 1000 atoms: 0.58 Number of scatterers: 8584 At special positions: 0 Unit cell: (116.833, 114.347, 100.261, 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 64 16.00 O 1588 8.00 N 1439 7.00 C 5493 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.01 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 3.24 Conformation dependent library (CDL) restraints added in 1.7 seconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 14 sheets defined 32.8% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'R' and resid 37 through 56 removed outlier: 3.521A pdb=" N LEU R 42 " --> pdb=" O LEU R 38 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL R 43 " --> pdb=" O PHE R 39 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE R 50 " --> pdb=" O VAL R 46 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY R 56 " --> pdb=" O LEU R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 94 Processing helix chain 'R' and resid 104 through 132 removed outlier: 3.716A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 138 Processing helix chain 'R' and resid 145 through 166 Processing helix chain 'R' and resid 180 through 211 Processing helix chain 'R' and resid 218 through 234 Processing helix chain 'R' and resid 237 through 244 Processing helix chain 'R' and resid 246 through 250 Processing helix chain 'R' and resid 254 through 278 removed outlier: 3.715A pdb=" N HIS R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'A' and resid 7 through 30 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.605A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.291A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 6.266A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 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 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 220 through 222 removed outlier: 3.584A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 224 through 226 removed outlier: 7.637A pdb=" N VAL A 225 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE A 267 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.858A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.320A 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: 6.965A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 202 removed outlier: 6.706A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.297A 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: 6.708A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.797A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.765A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 165 through 169 Processing sheet with id= K, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= L, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.517A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.639A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR S 216 " --> pdb=" O PHE S 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET S 218 " --> pdb=" O TYR S 163 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 143 through 148 removed outlier: 3.899A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER S 194 " --> pdb=" O THR S 201 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1071 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: 2.44 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2523 1.34 - 1.46: 2378 1.46 - 1.59: 3780 1.59 - 1.72: 1 1.72 - 1.85: 89 Bond restraints: 8771 Sorted by residual: bond pdb=" C PRO R 238 " pdb=" N PHE R 239 " ideal model delta sigma weight residual 1.335 1.471 -0.137 1.31e-02 5.83e+03 1.09e+02 bond pdb=" C GLY R 236 " pdb=" N LEU R 237 " ideal model delta sigma weight residual 1.331 1.440 -0.109 2.07e-02 2.33e+03 2.77e+01 bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.626 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.336 1.372 -0.036 1.20e-02 6.94e+03 9.25e+00 bond pdb=" CG LEU B 146 " pdb=" CD2 LEU B 146 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 8.99e+00 ... (remaining 8766 not shown) Histogram of bond angle deviations from ideal: 94.27 - 102.28: 34 102.28 - 110.28: 2149 110.28 - 118.28: 4483 118.28 - 126.29: 5057 126.29 - 134.29: 165 Bond angle restraints: 11888 Sorted by residual: angle pdb=" N ASP R 254 " pdb=" CA ASP R 254 " pdb=" C ASP R 254 " ideal model delta sigma weight residual 111.28 120.50 -9.22 1.09e+00 8.42e-01 7.16e+01 angle pdb=" C ASN R 275 " pdb=" N PRO R 276 " pdb=" CA PRO R 276 " ideal model delta sigma weight residual 119.47 111.39 8.08 1.16e+00 7.43e-01 4.86e+01 angle pdb=" CA PRO R 276 " pdb=" N PRO R 276 " pdb=" CD PRO R 276 " ideal model delta sigma weight residual 112.00 102.58 9.42 1.40e+00 5.10e-01 4.53e+01 angle pdb=" N GLN B 17 " pdb=" CA GLN B 17 " pdb=" CB GLN B 17 " ideal model delta sigma weight residual 110.16 119.85 -9.69 1.48e+00 4.57e-01 4.29e+01 angle pdb=" N PRO R 276 " pdb=" CA PRO R 276 " pdb=" C PRO R 276 " ideal model delta sigma weight residual 113.81 123.17 -9.36 1.45e+00 4.76e-01 4.17e+01 ... (remaining 11883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.51: 4518 14.51 - 29.02: 538 29.02 - 43.54: 128 43.54 - 58.05: 18 58.05 - 72.56: 10 Dihedral angle restraints: 5212 sinusoidal: 2050 harmonic: 3162 Sorted by residual: dihedral pdb=" CA PHE R 172 " pdb=" C PHE R 172 " pdb=" N SER R 173 " pdb=" CA SER R 173 " ideal model delta harmonic sigma weight residual -180.00 -137.80 -42.20 0 5.00e+00 4.00e-02 7.12e+01 dihedral pdb=" CA GLY B 185 " pdb=" C GLY B 185 " pdb=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta harmonic sigma weight residual 180.00 150.37 29.63 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 5209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1212 0.122 - 0.244: 124 0.244 - 0.366: 13 0.366 - 0.488: 2 0.488 - 0.610: 3 Chirality restraints: 1354 Sorted by residual: chirality pdb=" CA PRO R 276 " pdb=" N PRO R 276 " pdb=" C PRO R 276 " pdb=" CB PRO R 276 " both_signs ideal model delta sigma weight residual False 2.72 2.11 0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" CB VAL B 296 " pdb=" CA VAL B 296 " pdb=" CG1 VAL B 296 " pdb=" CG2 VAL B 296 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.54e+00 ... (remaining 1351 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 275 " 0.134 5.00e-02 4.00e+02 2.01e-01 6.47e+01 pdb=" N PRO R 276 " -0.348 5.00e-02 4.00e+02 pdb=" CA PRO R 276 " 0.104 5.00e-02 4.00e+02 pdb=" CD PRO R 276 " 0.110 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER R 273 " 0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C SER R 273 " -0.071 2.00e-02 2.50e+03 pdb=" O SER R 273 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA R 274 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 230 " -0.016 2.00e-02 2.50e+03 2.66e-02 1.41e+01 pdb=" CG TYR A 230 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR A 230 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 230 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 230 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 230 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 230 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 230 " 0.002 2.00e-02 2.50e+03 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 92 2.61 - 3.18: 6715 3.18 - 3.75: 13788 3.75 - 4.33: 18675 4.33 - 4.90: 31118 Nonbonded interactions: 70388 Sorted by model distance: nonbonded pdb=" O CYS R 258 " pdb=" CD PRO R 262 " model vdw 2.035 3.440 nonbonded pdb=" OD1 ASN R 48 " pdb=" CG PRO R 276 " model vdw 2.170 3.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.286 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.294 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.295 2.440 ... (remaining 70383 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: 0.410 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: 2.330 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.140 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.010 0.137 8771 Z= 0.677 Angle : 1.395 15.384 11888 Z= 0.754 Chirality : 0.082 0.610 1354 Planarity : 0.010 0.201 1489 Dihedral : 13.540 72.560 3162 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.39 % Allowed : 1.28 % Favored : 97.33 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.89 (0.23), residues: 1081 helix: -2.11 (0.22), residues: 355 sheet: -1.33 (0.30), residues: 276 loop : -1.94 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP R 133 HIS 0.026 0.004 HIS S 220 PHE 0.035 0.004 PHE R 50 TYR 0.064 0.005 TYR A 230 ARG 0.032 0.002 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 203 time to evaluate : 1.045 Fit side-chains REVERT: R 234 LEU cc_start: 0.8434 (mt) cc_final: 0.8093 (mp) REVERT: R 252 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6710 (m-30) REVERT: A 294 ASN cc_start: 0.6673 (m110) cc_final: 0.6360 (t0) REVERT: A 318 GLU cc_start: 0.6400 (tp30) cc_final: 0.6000 (tp30) REVERT: S 206 ARG cc_start: 0.7390 (mmt-90) cc_final: 0.7145 (mmp80) outliers start: 13 outliers final: 4 residues processed: 214 average time/residue: 1.2167 time to fit residues: 276.4579 Evaluate side-chains 153 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 252 ASP Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 271 ASN Chi-restraints excluded: chain R residue 276 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 ASN R 82 GLN R 275 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 183 HIS B 259 GLN B 268 ASN S 39 GLN S 159 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8771 Z= 0.193 Angle : 0.677 8.384 11888 Z= 0.345 Chirality : 0.045 0.339 1354 Planarity : 0.005 0.051 1489 Dihedral : 6.869 72.786 1254 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.31 % Allowed : 12.93 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.24), residues: 1081 helix: -0.29 (0.26), residues: 355 sheet: -1.05 (0.30), residues: 272 loop : -1.56 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 82 HIS 0.007 0.001 HIS A 213 PHE 0.018 0.001 PHE R 257 TYR 0.013 0.001 TYR A 296 ARG 0.011 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 1.021 Fit side-chains REVERT: R 196 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7757 (ttp) REVERT: R 250 TRP cc_start: 0.7191 (OUTLIER) cc_final: 0.6976 (t-100) REVERT: A 240 MET cc_start: 0.6083 (OUTLIER) cc_final: 0.5844 (tmt) REVERT: A 318 GLU cc_start: 0.6423 (tp30) cc_final: 0.5989 (tp30) REVERT: B 15 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7564 (mmmt) REVERT: B 16 ASN cc_start: 0.8580 (m-40) cc_final: 0.8221 (m110) REVERT: G 37 LEU cc_start: 0.7901 (mm) cc_final: 0.7675 (mm) REVERT: S 143 VAL cc_start: 0.6811 (t) cc_final: 0.6586 (m) REVERT: S 234 GLU cc_start: 0.5651 (pm20) cc_final: 0.5190 (pm20) outliers start: 31 outliers final: 8 residues processed: 198 average time/residue: 1.1347 time to fit residues: 240.4163 Evaluate side-chains 167 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 155 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 250 TRP Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 26 optimal weight: 0.1980 chunk 97 optimal weight: 40.0000 chunk 105 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 96 optimal weight: 0.1980 chunk 33 optimal weight: 0.0970 chunk 78 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 304 GLN A 331 ASN B 75 GLN B 259 GLN B 340 ASN G 59 ASN S 171 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8771 Z= 0.187 Angle : 0.635 8.438 11888 Z= 0.320 Chirality : 0.044 0.330 1354 Planarity : 0.004 0.041 1489 Dihedral : 6.112 74.058 1246 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.27 % Allowed : 16.88 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.96 (0.25), residues: 1081 helix: 0.54 (0.27), residues: 363 sheet: -0.91 (0.30), residues: 273 loop : -1.35 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 82 HIS 0.007 0.001 HIS A 213 PHE 0.010 0.001 PHE B 199 TYR 0.012 0.001 TYR S 161 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 170 time to evaluate : 1.049 Fit side-chains REVERT: R 199 CYS cc_start: 0.6935 (m) cc_final: 0.6731 (p) REVERT: A 33 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6259 (mp0) REVERT: A 240 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.6177 (tmt) REVERT: A 305 CYS cc_start: 0.7898 (m) cc_final: 0.7365 (m) REVERT: A 318 GLU cc_start: 0.6400 (tp30) cc_final: 0.6052 (tp30) REVERT: B 15 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7525 (mmmt) REVERT: B 16 ASN cc_start: 0.8691 (m-40) cc_final: 0.8314 (m110) REVERT: B 19 ARG cc_start: 0.7484 (mtm110) cc_final: 0.6925 (ttp80) REVERT: S 143 VAL cc_start: 0.6898 (t) cc_final: 0.6690 (m) outliers start: 40 outliers final: 15 residues processed: 188 average time/residue: 1.0536 time to fit residues: 212.6882 Evaluate side-chains 173 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 0.0870 chunk 103 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8771 Z= 0.267 Angle : 0.674 11.589 11888 Z= 0.336 Chirality : 0.045 0.338 1354 Planarity : 0.003 0.039 1489 Dihedral : 6.052 76.327 1246 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.85 % Allowed : 19.87 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.73 (0.26), residues: 1081 helix: 0.86 (0.28), residues: 363 sheet: -1.00 (0.30), residues: 275 loop : -1.17 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.007 0.001 HIS S 155 PHE 0.014 0.002 PHE S 165 TYR 0.024 0.002 TYR A 230 ARG 0.005 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 162 time to evaluate : 0.994 Fit side-chains REVERT: R 199 CYS cc_start: 0.7055 (m) cc_final: 0.6773 (p) REVERT: R 243 TRP cc_start: 0.7129 (t-100) cc_final: 0.6357 (t-100) REVERT: R 259 HIS cc_start: 0.6744 (OUTLIER) cc_final: 0.6303 (t-90) REVERT: A 33 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6292 (mp0) REVERT: A 294 ASN cc_start: 0.7140 (t0) cc_final: 0.6692 (t0) REVERT: A 318 GLU cc_start: 0.6465 (tp30) cc_final: 0.6045 (tp30) REVERT: B 15 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7514 (mmmt) REVERT: B 16 ASN cc_start: 0.8775 (m-40) cc_final: 0.8420 (m110) REVERT: B 19 ARG cc_start: 0.7429 (mtm110) cc_final: 0.6937 (ttp80) REVERT: B 262 MET cc_start: 0.7654 (mmm) cc_final: 0.7019 (tpt) REVERT: G 37 LEU cc_start: 0.7889 (mm) cc_final: 0.7623 (mm) REVERT: S 143 VAL cc_start: 0.6813 (t) cc_final: 0.6570 (m) REVERT: S 234 GLU cc_start: 0.5752 (pm20) cc_final: 0.5514 (pm20) outliers start: 36 outliers final: 16 residues processed: 176 average time/residue: 1.0852 time to fit residues: 204.4679 Evaluate side-chains 165 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 259 HIS Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8771 Z= 0.326 Angle : 0.712 11.635 11888 Z= 0.356 Chirality : 0.047 0.341 1354 Planarity : 0.004 0.038 1489 Dihedral : 6.079 76.510 1246 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.85 % Allowed : 22.22 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.73 (0.26), residues: 1081 helix: 0.94 (0.28), residues: 361 sheet: -1.12 (0.30), residues: 277 loop : -1.16 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 211 HIS 0.008 0.001 HIS S 155 PHE 0.015 0.002 PHE B 151 TYR 0.018 0.002 TYR S 59 ARG 0.007 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 0.949 Fit side-chains REVERT: R 243 TRP cc_start: 0.7151 (t-100) cc_final: 0.6388 (t-100) REVERT: R 259 HIS cc_start: 0.6810 (OUTLIER) cc_final: 0.6272 (t-90) REVERT: A 33 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6310 (mp0) REVERT: A 248 LYS cc_start: 0.8051 (tppt) cc_final: 0.7799 (mtpp) REVERT: A 294 ASN cc_start: 0.7236 (t0) cc_final: 0.6717 (t0) REVERT: A 318 GLU cc_start: 0.6517 (tp30) cc_final: 0.6117 (tp30) REVERT: B 4 LEU cc_start: 0.5365 (OUTLIER) cc_final: 0.5078 (tt) REVERT: B 15 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7458 (mmmt) REVERT: B 16 ASN cc_start: 0.8786 (m-40) cc_final: 0.8440 (m110) REVERT: B 19 ARG cc_start: 0.7443 (mtm110) cc_final: 0.6949 (ttp80) REVERT: B 82 TRP cc_start: 0.7683 (OUTLIER) cc_final: 0.7419 (m-10) REVERT: B 101 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8386 (ptp) REVERT: B 172 GLU cc_start: 0.7818 (pm20) cc_final: 0.7570 (pm20) REVERT: B 262 MET cc_start: 0.7610 (mmm) cc_final: 0.7175 (tpt) REVERT: S 143 VAL cc_start: 0.6819 (t) cc_final: 0.6537 (m) outliers start: 36 outliers final: 22 residues processed: 169 average time/residue: 1.0382 time to fit residues: 188.1166 Evaluate side-chains 173 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 259 HIS Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** 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: 0.7240 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8771 Z= 0.316 Angle : 0.704 11.099 11888 Z= 0.352 Chirality : 0.047 0.340 1354 Planarity : 0.003 0.037 1489 Dihedral : 6.039 76.099 1246 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.49 % Allowed : 23.50 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.66 (0.26), residues: 1081 helix: 1.05 (0.28), residues: 361 sheet: -1.11 (0.30), residues: 277 loop : -1.15 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 211 HIS 0.008 0.001 HIS S 155 PHE 0.015 0.002 PHE B 151 TYR 0.017 0.002 TYR S 59 ARG 0.007 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 0.993 Fit side-chains REVERT: R 158 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7721 (tt) REVERT: R 199 CYS cc_start: 0.7073 (m) cc_final: 0.6749 (p) REVERT: R 243 TRP cc_start: 0.7177 (t-100) cc_final: 0.6431 (t-100) REVERT: R 259 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.6296 (t-90) REVERT: A 33 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: A 53 MET cc_start: 0.8265 (mpt) cc_final: 0.7664 (mpt) REVERT: A 241 ASN cc_start: 0.8008 (m-40) cc_final: 0.7734 (t160) REVERT: A 294 ASN cc_start: 0.7155 (t0) cc_final: 0.6586 (t0) REVERT: A 318 GLU cc_start: 0.6527 (tp30) cc_final: 0.6131 (tp30) REVERT: B 15 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7464 (mmmt) REVERT: B 16 ASN cc_start: 0.8796 (m-40) cc_final: 0.8448 (m110) REVERT: B 19 ARG cc_start: 0.7397 (mtm110) cc_final: 0.6906 (ttp80) REVERT: B 82 TRP cc_start: 0.7590 (OUTLIER) cc_final: 0.7368 (m-10) REVERT: B 101 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8489 (ptp) REVERT: B 172 GLU cc_start: 0.7883 (pm20) cc_final: 0.7563 (pm20) REVERT: B 189 SER cc_start: 0.7413 (OUTLIER) cc_final: 0.7097 (t) REVERT: B 262 MET cc_start: 0.7571 (mmm) cc_final: 0.7153 (tpt) REVERT: S 143 VAL cc_start: 0.6755 (t) cc_final: 0.6522 (m) outliers start: 42 outliers final: 20 residues processed: 175 average time/residue: 1.0655 time to fit residues: 200.2206 Evaluate side-chains 170 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 259 HIS Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8771 Z= 0.284 Angle : 0.698 10.944 11888 Z= 0.348 Chirality : 0.046 0.351 1354 Planarity : 0.003 0.037 1489 Dihedral : 5.956 76.183 1246 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.49 % Allowed : 25.64 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.54 (0.26), residues: 1081 helix: 1.14 (0.28), residues: 361 sheet: -1.09 (0.30), residues: 282 loop : -1.02 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 211 HIS 0.007 0.001 HIS S 155 PHE 0.016 0.001 PHE R 244 TYR 0.015 0.002 TYR S 59 ARG 0.007 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 149 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: R 158 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7709 (tt) REVERT: R 199 CYS cc_start: 0.7073 (m) cc_final: 0.6780 (p) REVERT: A 33 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6274 (mp0) REVERT: A 53 MET cc_start: 0.8239 (mpt) cc_final: 0.7610 (mpt) REVERT: A 240 MET cc_start: 0.6198 (tmt) cc_final: 0.5980 (tmt) REVERT: A 241 ASN cc_start: 0.8034 (m-40) cc_final: 0.7426 (t0) REVERT: A 248 LYS cc_start: 0.8003 (tppt) cc_final: 0.7786 (mtpp) REVERT: A 294 ASN cc_start: 0.7121 (t0) cc_final: 0.6566 (t0) REVERT: A 318 GLU cc_start: 0.6550 (tp30) cc_final: 0.6172 (tp30) REVERT: B 4 LEU cc_start: 0.5047 (OUTLIER) cc_final: 0.4612 (tt) REVERT: B 15 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7458 (mmmt) REVERT: B 16 ASN cc_start: 0.8776 (m-40) cc_final: 0.8394 (m110) REVERT: B 19 ARG cc_start: 0.7335 (mtm110) cc_final: 0.6814 (ttp80) REVERT: B 20 ASP cc_start: 0.8381 (p0) cc_final: 0.8166 (p0) REVERT: B 101 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8495 (ptp) REVERT: B 172 GLU cc_start: 0.7930 (pm20) cc_final: 0.7546 (pm20) REVERT: B 189 SER cc_start: 0.7441 (OUTLIER) cc_final: 0.7163 (t) REVERT: B 262 MET cc_start: 0.7510 (mmm) cc_final: 0.7210 (tpt) REVERT: S 143 VAL cc_start: 0.6761 (t) cc_final: 0.6544 (m) outliers start: 42 outliers final: 25 residues processed: 175 average time/residue: 1.0469 time to fit residues: 197.2019 Evaluate side-chains 172 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 40.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8771 Z= 0.232 Angle : 0.687 11.152 11888 Z= 0.337 Chirality : 0.046 0.361 1354 Planarity : 0.003 0.040 1489 Dihedral : 5.837 76.235 1246 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.17 % Allowed : 26.50 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.41 (0.26), residues: 1081 helix: 1.23 (0.28), residues: 361 sheet: -0.95 (0.30), residues: 276 loop : -0.99 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 82 HIS 0.007 0.001 HIS S 155 PHE 0.013 0.001 PHE R 244 TYR 0.025 0.002 TYR A 230 ARG 0.008 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 145 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: R 158 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7681 (tt) REVERT: R 199 CYS cc_start: 0.7088 (m) cc_final: 0.6774 (p) REVERT: A 241 ASN cc_start: 0.8022 (m-40) cc_final: 0.7342 (t0) REVERT: A 294 ASN cc_start: 0.7108 (t0) cc_final: 0.6561 (t0) REVERT: A 318 GLU cc_start: 0.6499 (tp30) cc_final: 0.6246 (tp30) REVERT: B 4 LEU cc_start: 0.4963 (OUTLIER) cc_final: 0.4505 (tt) REVERT: B 15 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7421 (mmmt) REVERT: B 16 ASN cc_start: 0.8731 (m-40) cc_final: 0.8342 (m110) REVERT: B 19 ARG cc_start: 0.7286 (mtm110) cc_final: 0.6814 (ttp80) REVERT: B 20 ASP cc_start: 0.8334 (p0) cc_final: 0.8133 (p0) REVERT: B 172 GLU cc_start: 0.7884 (pm20) cc_final: 0.7442 (pm20) REVERT: B 262 MET cc_start: 0.7545 (mmm) cc_final: 0.7253 (tpt) REVERT: S 34 MET cc_start: 0.5729 (OUTLIER) cc_final: 0.5359 (tmt) REVERT: S 143 VAL cc_start: 0.6878 (t) cc_final: 0.6673 (m) outliers start: 39 outliers final: 22 residues processed: 167 average time/residue: 1.0788 time to fit residues: 193.5455 Evaluate side-chains 166 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.0570 chunk 96 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8771 Z= 0.263 Angle : 0.708 12.806 11888 Z= 0.351 Chirality : 0.047 0.387 1354 Planarity : 0.004 0.040 1489 Dihedral : 5.815 76.406 1245 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.53 % Allowed : 26.71 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.40 (0.26), residues: 1081 helix: 1.25 (0.28), residues: 361 sheet: -0.97 (0.30), residues: 281 loop : -0.96 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP B 82 HIS 0.007 0.001 HIS S 155 PHE 0.015 0.001 PHE R 244 TYR 0.014 0.002 TYR S 59 ARG 0.009 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: R 109 MET cc_start: 0.5606 (tpt) cc_final: 0.5355 (mmt) REVERT: R 158 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7687 (tt) REVERT: R 199 CYS cc_start: 0.7089 (m) cc_final: 0.6787 (p) REVERT: A 241 ASN cc_start: 0.7927 (m-40) cc_final: 0.7514 (t160) REVERT: A 294 ASN cc_start: 0.6911 (t0) cc_final: 0.6365 (t0) REVERT: A 318 GLU cc_start: 0.6509 (tp30) cc_final: 0.6290 (tp30) REVERT: B 15 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7429 (mmmt) REVERT: B 16 ASN cc_start: 0.8715 (m-40) cc_final: 0.8313 (m110) REVERT: B 19 ARG cc_start: 0.7310 (mtm110) cc_final: 0.6829 (ttp80) REVERT: B 20 ASP cc_start: 0.8335 (p0) cc_final: 0.8114 (p0) REVERT: B 262 MET cc_start: 0.7501 (mmm) cc_final: 0.7221 (tpt) REVERT: S 143 VAL cc_start: 0.6884 (t) cc_final: 0.6672 (m) REVERT: S 234 GLU cc_start: 0.6082 (pm20) cc_final: 0.5505 (pm20) outliers start: 33 outliers final: 24 residues processed: 163 average time/residue: 1.1251 time to fit residues: 196.9757 Evaluate side-chains 163 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 98 optimal weight: 40.0000 chunk 84 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8771 Z= 0.204 Angle : 0.697 11.797 11888 Z= 0.340 Chirality : 0.046 0.383 1354 Planarity : 0.003 0.044 1489 Dihedral : 5.692 76.329 1245 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.56 % Allowed : 28.10 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.27 (0.26), residues: 1081 helix: 1.30 (0.28), residues: 360 sheet: -0.83 (0.30), residues: 278 loop : -0.89 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 211 HIS 0.006 0.001 HIS A 213 PHE 0.016 0.001 PHE R 244 TYR 0.011 0.001 TYR S 102 ARG 0.008 0.000 ARG A 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 1.058 Fit side-chains REVERT: R 109 MET cc_start: 0.5607 (tpt) cc_final: 0.5359 (mmt) REVERT: R 158 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7618 (tt) REVERT: R 199 CYS cc_start: 0.7076 (m) cc_final: 0.6785 (p) REVERT: A 241 ASN cc_start: 0.7921 (m-40) cc_final: 0.7400 (t160) REVERT: A 294 ASN cc_start: 0.6873 (t0) cc_final: 0.6343 (t0) REVERT: A 297 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7683 (mm-30) REVERT: A 305 CYS cc_start: 0.8070 (m) cc_final: 0.7510 (m) REVERT: A 318 GLU cc_start: 0.6438 (tp30) cc_final: 0.6195 (tp30) REVERT: B 15 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7423 (mmmt) REVERT: B 16 ASN cc_start: 0.8711 (m-40) cc_final: 0.8295 (m110) REVERT: B 19 ARG cc_start: 0.7280 (mtm110) cc_final: 0.6816 (ttp80) REVERT: B 172 GLU cc_start: 0.7714 (pm20) cc_final: 0.7229 (pm20) REVERT: B 262 MET cc_start: 0.7466 (mmm) cc_final: 0.7218 (tpt) REVERT: G 21 MET cc_start: 0.8001 (ttm) cc_final: 0.7784 (ttm) REVERT: S 234 GLU cc_start: 0.6031 (pm20) cc_final: 0.5494 (pm20) outliers start: 24 outliers final: 17 residues processed: 172 average time/residue: 1.0949 time to fit residues: 202.0897 Evaluate side-chains 165 residues out of total 940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 196 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.0020 chunk 12 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 10 optimal weight: 0.0670 chunk 15 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.8130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.194765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.154211 restraints weight = 10691.219| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 2.93 r_work: 0.4127 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8771 Z= 0.191 Angle : 0.677 11.671 11888 Z= 0.332 Chirality : 0.045 0.385 1354 Planarity : 0.003 0.042 1489 Dihedral : 5.628 76.243 1245 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.56 % Allowed : 28.74 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.15 (0.26), residues: 1081 helix: 1.33 (0.28), residues: 360 sheet: -0.70 (0.30), residues: 277 loop : -0.79 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 82 HIS 0.006 0.001 HIS A 213 PHE 0.015 0.001 PHE R 244 TYR 0.021 0.002 TYR A 230 ARG 0.008 0.000 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3835.97 seconds wall clock time: 68 minutes 48.61 seconds (4128.61 seconds total)