Starting phenix.real_space_refine on Fri Dec 8 12:15:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/12_2023/7eo4_31226_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/12_2023/7eo4_31226.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/12_2023/7eo4_31226_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/12_2023/7eo4_31226_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/12_2023/7eo4_31226_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/12_2023/7eo4_31226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/12_2023/7eo4_31226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/12_2023/7eo4_31226_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eo4_31226/12_2023/7eo4_31226_neut_updated.pdb" } resolution = 2.86 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= 0.078 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: 5 Type Number sf(0) Gaussians S 58 5.16 5 C 5311 2.51 5 N 1399 2.21 5 O 1531 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "C ASP 76": "OD1" <-> "OD2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8302 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2247 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1205 Classifications: {'peptide': 151} Link IDs: {'TRANS': 150} Chain breaks: 4 Chain: "C" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'J8C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.87, per 1000 atoms: 0.59 Number of scatterers: 8302 At special positions: 0 Unit cell: (93.5, 123.2, 129.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 F 3 9.00 O 1531 8.00 N 1399 7.00 C 5311 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 191 " distance=2.04 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 3.12 Conformation dependent library (CDL) restraints added in 1.4 seconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 12 sheets defined 31.6% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 Processing helix chain 'A' and resid 47 through 71 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 79 through 104 removed outlier: 3.615A pdb=" N VAL A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 114 through 145 removed outlier: 4.004A pdb=" N ALA A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 178 removed outlier: 3.644A pdb=" N GLY A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU A 177 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 200 through 232 Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.938A pdb=" N ILE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.903A pdb=" N VAL A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 297 through 313 removed outlier: 3.777A pdb=" N ASN A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 316 through 322 Processing helix chain 'B' and resid 7 through 32 removed outlier: 4.049A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 50 No H-bonds generated for 'chain 'B' and resid 47 through 50' Processing helix chain 'B' and resid 251 through 254 No H-bonds generated for 'chain 'B' and resid 251 through 254' Processing helix chain 'B' and resid 329 through 350 removed outlier: 4.196A pdb=" N PHE B 334 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 removed outlier: 3.973A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing sheet with id= A, first strand: chain 'B' and resid 220 through 222 removed outlier: 4.191A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 37 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS B 195 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU B 36 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LYS B 197 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU B 38 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N PHE B 199 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 185 " --> pdb=" O ASP B 200 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.109A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.867A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.762A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.548A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 201 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.883A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE C 253 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 295 through 297 removed outlier: 3.533A pdb=" N ALA C 287 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.803A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.547A pdb=" N TRP E 36 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 128 through 130 removed outlier: 3.505A pdb=" N CYS E 147 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE E 200 " --> pdb=" O CYS E 147 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.554A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 912 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: 2.48 Time building geometry restraints manager: 3.38 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: 2587 1.34 - 1.46: 1992 1.46 - 1.58: 3806 1.58 - 1.71: 3 1.71 - 1.83: 81 Bond restraints: 8469 Sorted by residual: bond pdb=" C16 J8C A 401 " pdb=" C19 J8C A 401 " ideal model delta sigma weight residual 0.000 1.576 -1.576 2.00e-02 2.50e+03 6.21e+03 bond pdb=" C12 J8C A 401 " pdb=" C13 J8C A 401 " ideal model delta sigma weight residual 1.958 1.584 0.374 2.00e-02 2.50e+03 3.49e+02 bond pdb=" C02 J8C A 401 " pdb=" C03 J8C A 401 " ideal model delta sigma weight residual 1.428 1.563 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C19 J8C A 401 " pdb=" C20 J8C A 401 " ideal model delta sigma weight residual 1.457 1.585 -0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" N10 J8C A 401 " pdb=" O11 J8C A 401 " ideal model delta sigma weight residual 1.523 1.408 0.115 2.00e-02 2.50e+03 3.33e+01 ... (remaining 8464 not shown) Histogram of bond angle deviations from ideal: 87.26 - 96.64: 4 96.64 - 106.02: 138 106.02 - 115.39: 5192 115.39 - 124.77: 5976 124.77 - 134.15: 162 Bond angle restraints: 11472 Sorted by residual: angle pdb=" C12 J8C A 401 " pdb=" C13 J8C A 401 " pdb=" C14 J8C A 401 " ideal model delta sigma weight residual 105.15 120.45 -15.30 3.00e+00 1.11e-01 2.60e+01 angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" CB MET E 180 " ideal model delta sigma weight residual 114.17 108.76 5.41 1.14e+00 7.69e-01 2.25e+01 angle pdb=" N ASP C 303 " pdb=" CA ASP C 303 " pdb=" C ASP C 303 " ideal model delta sigma weight residual 107.48 117.67 -10.19 2.29e+00 1.91e-01 1.98e+01 angle pdb=" N ASP E 211 " pdb=" CA ASP E 211 " pdb=" C ASP E 211 " ideal model delta sigma weight residual 110.80 101.34 9.46 2.13e+00 2.20e-01 1.97e+01 angle pdb=" N PHE C 292 " pdb=" CA PHE C 292 " pdb=" CB PHE C 292 " ideal model delta sigma weight residual 114.17 109.11 5.06 1.14e+00 7.69e-01 1.97e+01 ... (remaining 11467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.93: 4719 22.93 - 45.86: 243 45.86 - 68.79: 25 68.79 - 91.72: 6 91.72 - 114.65: 4 Dihedral angle restraints: 4997 sinusoidal: 1932 harmonic: 3065 Sorted by residual: dihedral pdb=" C ASP E 211 " pdb=" N ASP E 211 " pdb=" CA ASP E 211 " pdb=" CB ASP E 211 " ideal model delta harmonic sigma weight residual -122.60 -112.23 -10.37 0 2.50e+00 1.60e-01 1.72e+01 dihedral pdb=" CA THR B 187 " pdb=" C THR B 187 " pdb=" N HIS B 188 " pdb=" CA HIS B 188 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TRP C 339 " pdb=" C TRP C 339 " pdb=" N ASN C 340 " pdb=" CA ASN C 340 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.173: 1323 1.173 - 2.347: 0 2.347 - 3.520: 0 3.520 - 4.693: 0 4.693 - 5.866: 1 Chirality restraints: 1324 Sorted by residual: chirality pdb=" C33 J8C A 401 " pdb=" C32 J8C A 401 " pdb=" C34 J8C A 401 " pdb=" C35 J8C A 401 " both_signs ideal model delta sigma weight residual False -2.82 3.05 -5.87 2.00e-01 2.50e+01 8.60e+02 chirality pdb=" CA ASP E 211 " pdb=" N ASP E 211 " pdb=" C ASP E 211 " pdb=" CB ASP E 211 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA ALA E 209 " pdb=" N ALA E 209 " pdb=" C ALA E 209 " pdb=" CB ALA E 209 " both_signs ideal model delta sigma weight residual False 2.48 2.74 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1321 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 292 " -0.291 9.50e-02 1.11e+02 1.31e-01 1.05e+01 pdb=" NE ARG A 292 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 292 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 292 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 292 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.74e+00 pdb=" N PRO C 236 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 177 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.61e+00 pdb=" N PRO A 178 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " 0.039 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1250 2.76 - 3.29: 7641 3.29 - 3.83: 12511 3.83 - 4.36: 14972 4.36 - 4.90: 26009 Nonbonded interactions: 62383 Sorted by model distance: nonbonded pdb=" N GLY C 144 " pdb=" OD1 ASP C 163 " model vdw 2.220 2.520 nonbonded pdb=" O GLY E 197 " pdb=" OG1 THR E 198 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.244 2.440 nonbonded pdb=" O LEU C 30 " pdb=" OG1 THR C 34 " model vdw 2.274 2.440 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.297 2.440 ... (remaining 62378 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.150 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.850 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 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 : 0.019 1.576 8469 Z= 1.552 Angle : 1.004 15.296 11472 Z= 0.538 Chirality : 0.170 5.866 1324 Planarity : 0.007 0.131 1424 Dihedral : 14.176 114.647 3008 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1033 helix: 1.19 (0.29), residues: 312 sheet: -1.83 (0.30), residues: 239 loop : -1.84 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 63 HIS 0.011 0.002 HIS B 213 PHE 0.040 0.003 PHE C 151 TYR 0.023 0.003 TYR A 31 ARG 0.011 0.001 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.953 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 1.0872 time to fit residues: 201.5107 Evaluate side-chains 148 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 237 ASN C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.0572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 8469 Z= 0.404 Angle : 1.139 24.209 11472 Z= 0.543 Chirality : 0.072 1.987 1324 Planarity : 0.007 0.068 1424 Dihedral : 9.270 106.608 1155 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.65 % Allowed : 10.39 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.30 (0.25), residues: 1033 helix: 1.22 (0.29), residues: 311 sheet: -1.60 (0.30), residues: 247 loop : -1.88 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 63 HIS 0.008 0.002 HIS B 213 PHE 0.033 0.002 PHE C 151 TYR 0.016 0.002 TYR E 103 ARG 0.013 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 0.980 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 153 average time/residue: 1.1347 time to fit residues: 185.9642 Evaluate side-chains 158 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 7 residues processed: 9 average time/residue: 0.3652 time to fit residues: 5.2021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 94 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.0589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 8469 Z= 0.404 Angle : 1.139 24.209 11472 Z= 0.543 Chirality : 0.072 1.987 1324 Planarity : 0.007 0.068 1424 Dihedral : 9.271 106.608 1155 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.88 % Allowed : 12.60 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.30 (0.25), residues: 1033 helix: 1.22 (0.29), residues: 311 sheet: -1.60 (0.30), residues: 247 loop : -1.88 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 63 HIS 0.008 0.002 HIS B 213 PHE 0.033 0.002 PHE C 151 TYR 0.016 0.002 TYR E 103 ARG 0.013 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 0.848 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 150 average time/residue: 1.1028 time to fit residues: 177.3703 Evaluate side-chains 149 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.2986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.0588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 8469 Z= 0.404 Angle : 1.139 24.208 11472 Z= 0.543 Chirality : 0.072 1.987 1324 Planarity : 0.007 0.068 1424 Dihedral : 9.270 106.608 1155 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.88 % Allowed : 12.71 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.30 (0.25), residues: 1033 helix: 1.22 (0.29), residues: 311 sheet: -1.60 (0.30), residues: 247 loop : -1.88 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 63 HIS 0.008 0.002 HIS B 213 PHE 0.033 0.002 PHE C 151 TYR 0.016 0.002 TYR E 103 ARG 0.013 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 0.921 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 150 average time/residue: 1.0748 time to fit residues: 172.9125 Evaluate side-chains 149 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.2882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 69 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.0588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.137 8469 Z= 0.404 Angle : 1.139 24.201 11472 Z= 0.543 Chirality : 0.072 1.986 1324 Planarity : 0.007 0.068 1424 Dihedral : 9.266 106.601 1155 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.88 % Allowed : 12.71 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.30 (0.25), residues: 1033 helix: 1.22 (0.29), residues: 311 sheet: -1.60 (0.30), residues: 247 loop : -1.88 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 63 HIS 0.008 0.002 HIS B 213 PHE 0.033 0.002 PHE C 151 TYR 0.016 0.002 TYR E 103 ARG 0.013 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 0.943 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 150 average time/residue: 1.1112 time to fit residues: 178.3550 Evaluate side-chains 149 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 0.823 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.2775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.0588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 8469 Z= 0.401 Angle : 1.138 23.974 11472 Z= 0.541 Chirality : 0.072 1.980 1324 Planarity : 0.007 0.068 1424 Dihedral : 9.198 106.415 1155 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.88 % Allowed : 12.71 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.30 (0.25), residues: 1033 helix: 1.22 (0.29), residues: 311 sheet: -1.59 (0.30), residues: 247 loop : -1.87 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 63 HIS 0.008 0.002 HIS B 213 PHE 0.033 0.002 PHE C 151 TYR 0.016 0.002 TYR E 103 ARG 0.013 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 0.866 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 150 average time/residue: 1.0706 time to fit residues: 172.3482 Evaluate side-chains 149 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.3029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 0.0970 chunk 56 optimal weight: 0.0770 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 8469 Z= 0.207 Angle : 0.686 9.501 11472 Z= 0.354 Chirality : 0.044 0.172 1324 Planarity : 0.005 0.061 1424 Dihedral : 6.664 82.763 1155 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.66 % Allowed : 12.38 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.68 (0.25), residues: 1033 helix: 1.51 (0.29), residues: 312 sheet: -0.59 (0.30), residues: 257 loop : -1.77 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.007 0.001 HIS E 35 PHE 0.016 0.002 PHE C 199 TYR 0.014 0.001 TYR A 295 ARG 0.009 0.001 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 0.922 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 165 average time/residue: 1.0085 time to fit residues: 179.3942 Evaluate side-chains 158 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 2 residues processed: 7 average time/residue: 0.2694 time to fit residues: 3.6492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 8469 Z= 0.218 Angle : 0.669 10.986 11472 Z= 0.347 Chirality : 0.044 0.180 1324 Planarity : 0.005 0.060 1424 Dihedral : 6.404 81.484 1155 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.77 % Allowed : 15.58 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.54 (0.26), residues: 1033 helix: 1.66 (0.29), residues: 313 sheet: -0.44 (0.30), residues: 257 loop : -1.77 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.006 0.001 HIS E 35 PHE 0.019 0.002 PHE C 151 TYR 0.016 0.002 TYR A 81 ARG 0.005 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 0.934 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 150 average time/residue: 1.1203 time to fit residues: 179.7462 Evaluate side-chains 149 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 142 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 0.1254 time to fit residues: 1.8510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8469 Z= 0.177 Angle : 0.631 13.686 11472 Z= 0.321 Chirality : 0.042 0.169 1324 Planarity : 0.005 0.061 1424 Dihedral : 6.130 83.329 1155 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.10 % Allowed : 16.46 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.32 (0.26), residues: 1033 helix: 1.87 (0.29), residues: 313 sheet: -0.22 (0.31), residues: 252 loop : -1.72 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.015 0.001 PHE A 322 TYR 0.013 0.001 TYR A 295 ARG 0.011 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 0.917 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 153 average time/residue: 1.0119 time to fit residues: 166.6654 Evaluate side-chains 148 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0975 time to fit residues: 1.5732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN C 237 ASN C 239 ASN D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8469 Z= 0.193 Angle : 0.630 10.121 11472 Z= 0.323 Chirality : 0.042 0.162 1324 Planarity : 0.005 0.058 1424 Dihedral : 6.003 83.925 1155 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.33 % Allowed : 16.69 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.18 (0.26), residues: 1033 helix: 2.04 (0.29), residues: 313 sheet: -0.09 (0.31), residues: 252 loop : -1.71 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.017 0.002 PHE C 151 TYR 0.015 0.001 TYR A 81 ARG 0.011 0.000 ARG A 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 0.943 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 149 average time/residue: 1.1289 time to fit residues: 180.2231 Evaluate side-chains 149 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.1449 time to fit residues: 2.0235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 0.0270 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN C 220 GLN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.229522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.192946 restraints weight = 16094.241| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.59 r_work: 0.3681 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 8469 Z= 0.200 Angle : 0.649 12.121 11472 Z= 0.328 Chirality : 0.042 0.160 1324 Planarity : 0.005 0.058 1424 Dihedral : 5.960 84.141 1155 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.22 % Allowed : 17.13 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.20 (0.26), residues: 1033 helix: 1.98 (0.29), residues: 313 sheet: -0.12 (0.31), residues: 257 loop : -1.69 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.006 0.001 HIS E 35 PHE 0.017 0.002 PHE C 151 TYR 0.013 0.001 TYR A 81 ARG 0.008 0.000 ARG A 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3316.26 seconds wall clock time: 59 minutes 37.89 seconds (3577.89 seconds total)