Starting phenix.real_space_refine on Tue Feb 13 18:18:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gdg_4390/02_2024/6gdg_4390_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gdg_4390/02_2024/6gdg_4390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gdg_4390/02_2024/6gdg_4390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gdg_4390/02_2024/6gdg_4390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gdg_4390/02_2024/6gdg_4390_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gdg_4390/02_2024/6gdg_4390_updated.pdb" } resolution = 4.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 49 5.16 5 C 4611 2.51 5 N 1246 2.21 5 O 1317 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D ARG 255": "NH1" <-> "NH2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7223 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1913 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 98 Chain: "B" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2377 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 14, 'ASN:plan1': 4, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 157 Chain: "C" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 262 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1721 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 98 Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 928 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.95, per 1000 atoms: 0.69 Number of scatterers: 7223 At special positions: 0 Unit cell: (92.02, 125.19, 78.11, 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 49 16.00 O 1317 8.00 N 1246 7.00 C 4611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " 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: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1874 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 11 sheets defined 37.6% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.853A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 58 removed outlier: 3.510A pdb=" N PHE A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.791A pdb=" N ILE A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 107 removed outlier: 3.612A pdb=" N ILE A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 No H-bonds generated for 'chain 'A' and resid 112 through 115' Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'A' and resid 168 through 171 No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 187 through 208 Processing helix chain 'A' and resid 225 through 258 removed outlier: 3.782A pdb=" N PHE A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 267 through 287 removed outlier: 3.858A pdb=" N ASN A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.984A pdb=" N GLN A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 298' Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.557A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 23 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'D' and resid 13 through 39 removed outlier: 3.803A pdb=" N LYS D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 235 through 237 No H-bonds generated for 'chain 'D' and resid 235 through 237' Processing helix chain 'D' and resid 253 through 268 removed outlier: 3.813A pdb=" N GLN D 257 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU D 258 " --> pdb=" O ASN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 293 removed outlier: 3.520A pdb=" N LYS D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 301 No H-bonds generated for 'chain 'D' and resid 298 through 301' Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 322 through 340 removed outlier: 3.546A pdb=" N ILE D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 335 " --> pdb=" O ILE D 331 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 380 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 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.965A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.099A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.630A pdb=" N SER B 147 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.160A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.657A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 327 through 329 removed outlier: 3.657A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 249 through 254 removed outlier: 3.706A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 41 through 44 removed outlier: 3.758A pdb=" N PHE D 212 " --> pdb=" O PHE D 219 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 247 through 249 removed outlier: 6.524A pdb=" N PHE D 280 " --> pdb=" O VAL D 248 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.626A pdb=" N SER E 71 " --> pdb=" O TYR E 80 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.549A pdb=" N THR E 122 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) 317 hydrogen bonds defined for protein. 927 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: 2.69 Time building geometry restraints manager: 3.06 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: 2335 1.34 - 1.46: 906 1.46 - 1.58: 4070 1.58 - 1.70: 0 1.70 - 1.81: 65 Bond restraints: 7376 Sorted by residual: bond pdb=" C4 NEC A 400 " pdb=" C5 NEC A 400 " ideal model delta sigma weight residual 1.385 1.474 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C5 NEC A 400 " pdb=" C6 NEC A 400 " ideal model delta sigma weight residual 1.407 1.488 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" CA VAL A 188 " pdb=" CB VAL A 188 " ideal model delta sigma weight residual 1.539 1.560 -0.021 5.40e-03 3.43e+04 1.47e+01 bond pdb=" C8 NEC A 400 " pdb=" N7 NEC A 400 " ideal model delta sigma weight residual 1.302 1.359 -0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" CA ILE A 64 " pdb=" CB ILE A 64 " ideal model delta sigma weight residual 1.540 1.571 -0.031 1.25e-02 6.40e+03 6.01e+00 ... (remaining 7371 not shown) Histogram of bond angle deviations from ideal: 99.93 - 107.22: 196 107.22 - 114.51: 4180 114.51 - 121.81: 3467 121.81 - 129.10: 2182 129.10 - 136.39: 57 Bond angle restraints: 10082 Sorted by residual: angle pdb=" N ASP D 229 " pdb=" CA ASP D 229 " pdb=" C ASP D 229 " ideal model delta sigma weight residual 112.38 118.19 -5.81 1.22e+00 6.72e-01 2.26e+01 angle pdb=" CA VAL A 188 " pdb=" C VAL A 188 " pdb=" N PRO A 189 " ideal model delta sigma weight residual 120.83 118.29 2.54 6.10e-01 2.69e+00 1.73e+01 angle pdb=" N SER B 161 " pdb=" CA SER B 161 " pdb=" C SER B 161 " ideal model delta sigma weight residual 108.38 113.47 -5.09 1.35e+00 5.49e-01 1.42e+01 angle pdb=" C PHE D 302 " pdb=" N PRO D 303 " pdb=" CA PRO D 303 " ideal model delta sigma weight residual 119.47 123.82 -4.35 1.16e+00 7.43e-01 1.40e+01 angle pdb=" N THR E 104 " pdb=" CA THR E 104 " pdb=" C THR E 104 " ideal model delta sigma weight residual 108.38 113.31 -4.93 1.35e+00 5.49e-01 1.34e+01 ... (remaining 10077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 3959 16.99 - 33.99: 266 33.99 - 50.98: 66 50.98 - 67.97: 12 67.97 - 84.96: 4 Dihedral angle restraints: 4307 sinusoidal: 1411 harmonic: 2896 Sorted by residual: dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 146 " pdb=" CB CYS A 146 " ideal model delta sinusoidal sigma weight residual 93.00 177.96 -84.96 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual -86.00 -163.29 77.29 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CA THR B 159 " pdb=" C THR B 159 " pdb=" N SER B 160 " pdb=" CA SER B 160 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 4304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 703 0.044 - 0.087: 338 0.087 - 0.131: 105 0.131 - 0.174: 37 0.174 - 0.218: 15 Chirality restraints: 1198 Sorted by residual: chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA VAL E 37 " pdb=" N VAL E 37 " pdb=" C VAL E 37 " pdb=" CB VAL E 37 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA TRP D 234 " pdb=" N TRP D 234 " pdb=" C TRP D 234 " pdb=" CB TRP D 234 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1195 not shown) Planarity restraints: 1283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 188 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 189 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 189 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 189 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 284 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO A 285 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 138 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO A 139 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " 0.025 5.00e-02 4.00e+02 ... (remaining 1280 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 2883 2.94 - 3.43: 7414 3.43 - 3.92: 12011 3.92 - 4.41: 13382 4.41 - 4.90: 22757 Nonbonded interactions: 58447 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.449 2.440 nonbonded pdb=" OG1 THR E 104 " pdb=" OD1 ASP E 106 " model vdw 2.471 2.440 nonbonded pdb=" OG SER B 227 " pdb=" OH TYR E 32 " model vdw 2.486 2.440 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.509 2.520 nonbonded pdb=" O GLN D 380 " pdb=" OE1 GLU D 382 " model vdw 2.537 3.040 ... (remaining 58442 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 1.190 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 25.030 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 7376 Z= 0.519 Angle : 1.103 9.859 10082 Z= 0.740 Chirality : 0.061 0.218 1198 Planarity : 0.004 0.052 1283 Dihedral : 13.001 79.978 2418 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.51 % Allowed : 4.89 % Favored : 94.60 % Rotamer: Outliers : 2.07 % Allowed : 6.80 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.21), residues: 981 helix: -1.30 (0.21), residues: 357 sheet: -2.83 (0.35), residues: 135 loop : -2.46 (0.23), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 234 HIS 0.003 0.001 HIS C 44 PHE 0.014 0.002 PHE D 208 TYR 0.009 0.001 TYR B 124 ARG 0.003 0.001 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 306 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.8227 (t) cc_final: 0.7849 (p) REVERT: A 34 ASN cc_start: 0.7194 (t0) cc_final: 0.6900 (t0) REVERT: A 38 GLN cc_start: 0.8132 (pt0) cc_final: 0.7557 (pt0) REVERT: A 82 CYS cc_start: 0.8532 (m) cc_final: 0.8010 (t) REVERT: A 129 TRP cc_start: 0.6886 (m100) cc_final: 0.6671 (m-10) REVERT: A 135 ILE cc_start: 0.8309 (mt) cc_final: 0.8091 (tt) REVERT: A 145 ASN cc_start: 0.7660 (t0) cc_final: 0.6839 (p0) REVERT: A 193 MET cc_start: 0.7549 (mtp) cc_final: 0.7347 (mtm) REVERT: A 199 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7934 (ttp-110) REVERT: A 290 TYR cc_start: 0.8656 (t80) cc_final: 0.8406 (t80) REVERT: B 111 TYR cc_start: 0.8582 (m-80) cc_final: 0.8201 (m-80) REVERT: B 125 ASN cc_start: 0.7963 (t0) cc_final: 0.7606 (p0) REVERT: B 187 VAL cc_start: 0.8688 (t) cc_final: 0.8405 (t) REVERT: B 218 CYS cc_start: 0.8586 (t) cc_final: 0.8335 (t) REVERT: B 290 ASP cc_start: 0.7257 (m-30) cc_final: 0.7033 (m-30) REVERT: B 325 MET cc_start: 0.8631 (ttm) cc_final: 0.8105 (tpt) REVERT: C 21 MET cc_start: 0.6129 (ttm) cc_final: 0.5835 (mmm) REVERT: D 17 LYS cc_start: 0.9269 (ttmt) cc_final: 0.8709 (tppt) REVERT: D 252 ASP cc_start: 0.8738 (m-30) cc_final: 0.8306 (t0) REVERT: D 268 ASN cc_start: 0.9355 (m-40) cc_final: 0.9154 (m-40) REVERT: D 270 ARG cc_start: 0.8458 (ttt180) cc_final: 0.8146 (ttt90) REVERT: D 272 LEU cc_start: 0.9230 (mt) cc_final: 0.9007 (mp) REVERT: D 334 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7827 (mm-30) REVERT: D 346 ARG cc_start: 0.8970 (mtt180) cc_final: 0.8735 (mtp85) REVERT: D 361 ASN cc_start: 0.8566 (m-40) cc_final: 0.8265 (m110) REVERT: D 383 LEU cc_start: 0.7660 (tp) cc_final: 0.7437 (mt) REVERT: E 20 LEU cc_start: 0.7879 (mt) cc_final: 0.7590 (mt) REVERT: E 60 TYR cc_start: 0.9074 (m-80) cc_final: 0.8525 (m-80) REVERT: E 68 PHE cc_start: 0.8183 (m-10) cc_final: 0.6736 (m-10) REVERT: E 69 THR cc_start: 0.8530 (m) cc_final: 0.8164 (p) REVERT: E 72 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7621 (ttm110) REVERT: E 74 ASN cc_start: 0.6871 (m-40) cc_final: 0.6050 (t0) REVERT: E 80 TYR cc_start: 0.7377 (m-80) cc_final: 0.6911 (m-80) outliers start: 14 outliers final: 4 residues processed: 315 average time/residue: 0.1922 time to fit residues: 79.1610 Evaluate side-chains 189 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 347 HIS E 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7376 Z= 0.193 Angle : 0.591 9.792 10082 Z= 0.314 Chirality : 0.043 0.169 1198 Planarity : 0.005 0.066 1283 Dihedral : 5.320 34.351 1084 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.30 % Allowed : 3.55 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.51 (0.24), residues: 981 helix: 0.52 (0.25), residues: 374 sheet: -2.03 (0.32), residues: 193 loop : -1.86 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 339 HIS 0.016 0.002 HIS D 347 PHE 0.012 0.002 PHE D 330 TYR 0.024 0.001 TYR B 59 ARG 0.005 0.001 ARG D 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 229 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LEU cc_start: 0.6850 (mt) cc_final: 0.6647 (pp) REVERT: A 145 ASN cc_start: 0.7539 (t0) cc_final: 0.6694 (p0) REVERT: A 182 PHE cc_start: 0.8530 (t80) cc_final: 0.8195 (t80) REVERT: A 197 TYR cc_start: 0.8198 (m-10) cc_final: 0.7947 (m-10) REVERT: A 199 ARG cc_start: 0.7678 (ttm110) cc_final: 0.7476 (ttm110) REVERT: A 276 LEU cc_start: 0.8822 (tp) cc_final: 0.8530 (tp) REVERT: B 43 ILE cc_start: 0.7332 (tp) cc_final: 0.6993 (mm) REVERT: B 111 TYR cc_start: 0.8354 (m-80) cc_final: 0.7869 (m-80) REVERT: B 166 CYS cc_start: 0.8705 (m) cc_final: 0.8452 (m) REVERT: B 187 VAL cc_start: 0.8922 (t) cc_final: 0.8712 (t) REVERT: B 188 MET cc_start: 0.8762 (mmm) cc_final: 0.8549 (mmm) REVERT: B 332 TRP cc_start: 0.9175 (m-10) cc_final: 0.8948 (m-10) REVERT: C 36 ASP cc_start: 0.8386 (t0) cc_final: 0.8176 (t70) REVERT: D 17 LYS cc_start: 0.9218 (ttmt) cc_final: 0.8802 (tppt) REVERT: D 233 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8278 (mmtm) REVERT: D 239 ASN cc_start: 0.8962 (p0) cc_final: 0.8411 (p0) REVERT: D 252 ASP cc_start: 0.8673 (m-30) cc_final: 0.8283 (t0) REVERT: E 32 TYR cc_start: 0.8470 (m-80) cc_final: 0.8194 (m-80) REVERT: E 60 TYR cc_start: 0.9152 (m-80) cc_final: 0.8603 (m-80) REVERT: E 69 THR cc_start: 0.8731 (m) cc_final: 0.8328 (p) REVERT: E 74 ASN cc_start: 0.6422 (m-40) cc_final: 0.6213 (m-40) outliers start: 2 outliers final: 1 residues processed: 231 average time/residue: 0.1725 time to fit residues: 55.2672 Evaluate side-chains 165 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 95 optimal weight: 0.3980 chunk 78 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN E 31 ASN E 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7376 Z= 0.265 Angle : 0.604 11.456 10082 Z= 0.320 Chirality : 0.043 0.163 1198 Planarity : 0.005 0.049 1283 Dihedral : 5.071 35.401 1084 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.81 (0.26), residues: 981 helix: 1.12 (0.27), residues: 370 sheet: -1.77 (0.33), residues: 195 loop : -1.38 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.008 0.002 HIS D 347 PHE 0.014 0.002 PHE A 257 TYR 0.025 0.002 TYR B 59 ARG 0.007 0.001 ARG D 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 137 LEU cc_start: 0.7202 (mt) cc_final: 0.6895 (pp) REVERT: A 140 MET cc_start: 0.7581 (mmt) cc_final: 0.7109 (mmt) REVERT: A 145 ASN cc_start: 0.7531 (t0) cc_final: 0.6698 (p0) REVERT: A 185 CYS cc_start: 0.9328 (m) cc_final: 0.9071 (m) REVERT: A 276 LEU cc_start: 0.8982 (tp) cc_final: 0.8671 (tp) REVERT: B 46 ARG cc_start: 0.8349 (mtt180) cc_final: 0.7586 (mmp-170) REVERT: B 111 TYR cc_start: 0.8451 (m-80) cc_final: 0.7978 (m-80) REVERT: B 188 MET cc_start: 0.8771 (mmm) cc_final: 0.8554 (mmm) REVERT: B 230 ASN cc_start: 0.8273 (m-40) cc_final: 0.8022 (m110) REVERT: B 262 MET cc_start: 0.8552 (tpp) cc_final: 0.8287 (tpp) REVERT: B 291 ASP cc_start: 0.7839 (p0) cc_final: 0.7586 (t0) REVERT: C 21 MET cc_start: 0.5277 (ttt) cc_final: 0.4975 (mmm) REVERT: D 17 LYS cc_start: 0.9243 (ttmt) cc_final: 0.8835 (tppt) REVERT: D 217 VAL cc_start: 0.8207 (t) cc_final: 0.7910 (p) REVERT: D 222 PHE cc_start: 0.6700 (t80) cc_final: 0.5839 (t80) REVERT: D 233 LYS cc_start: 0.9062 (mmmt) cc_final: 0.8733 (mmtt) REVERT: D 239 ASN cc_start: 0.9024 (p0) cc_final: 0.8521 (p0) REVERT: D 252 ASP cc_start: 0.8632 (m-30) cc_final: 0.8249 (t0) REVERT: D 269 ASN cc_start: 0.8944 (t0) cc_final: 0.8621 (t0) REVERT: E 32 TYR cc_start: 0.8555 (m-80) cc_final: 0.8249 (m-80) REVERT: E 69 THR cc_start: 0.8690 (m) cc_final: 0.8484 (p) REVERT: E 74 ASN cc_start: 0.6716 (m-40) cc_final: 0.6020 (m-40) REVERT: E 122 THR cc_start: 0.7499 (m) cc_final: 0.7130 (p) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1774 time to fit residues: 48.8418 Evaluate side-chains 146 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 25 optimal weight: 0.0970 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN C 18 GLN E 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7376 Z= 0.241 Angle : 0.566 7.834 10082 Z= 0.301 Chirality : 0.042 0.204 1198 Planarity : 0.004 0.049 1283 Dihedral : 4.985 44.018 1084 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.15 % Allowed : 4.29 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.26), residues: 981 helix: 1.36 (0.27), residues: 376 sheet: -1.66 (0.32), residues: 213 loop : -1.22 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.006 0.001 HIS D 347 PHE 0.018 0.002 PHE E 68 TYR 0.023 0.001 TYR B 59 ARG 0.004 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LEU cc_start: 0.7291 (mt) cc_final: 0.6987 (pp) REVERT: A 140 MET cc_start: 0.7388 (mmt) cc_final: 0.6820 (mmt) REVERT: A 145 ASN cc_start: 0.7538 (t0) cc_final: 0.6702 (p0) REVERT: A 174 MET cc_start: 0.8701 (mmm) cc_final: 0.8403 (tpp) REVERT: A 276 LEU cc_start: 0.8976 (tp) cc_final: 0.8691 (tp) REVERT: B 46 ARG cc_start: 0.8553 (mtt180) cc_final: 0.7766 (mmp-170) REVERT: B 82 TRP cc_start: 0.8773 (m100) cc_final: 0.8562 (m100) REVERT: B 111 TYR cc_start: 0.8548 (m-80) cc_final: 0.8063 (m-80) REVERT: B 188 MET cc_start: 0.8906 (mmm) cc_final: 0.8607 (mmm) REVERT: B 230 ASN cc_start: 0.8183 (m-40) cc_final: 0.7947 (m110) REVERT: B 259 GLN cc_start: 0.8414 (tt0) cc_final: 0.8162 (tt0) REVERT: B 262 MET cc_start: 0.8528 (tpp) cc_final: 0.8250 (tpp) REVERT: B 332 TRP cc_start: 0.9049 (m-10) cc_final: 0.8756 (m-10) REVERT: C 21 MET cc_start: 0.5166 (ttt) cc_final: 0.4931 (mmm) REVERT: D 17 LYS cc_start: 0.9201 (ttmt) cc_final: 0.8806 (tppt) REVERT: D 217 VAL cc_start: 0.8128 (t) cc_final: 0.7868 (p) REVERT: D 220 HIS cc_start: 0.7246 (t70) cc_final: 0.6894 (m170) REVERT: D 222 PHE cc_start: 0.6662 (t80) cc_final: 0.5908 (t80) REVERT: D 233 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8801 (mmtt) REVERT: D 239 ASN cc_start: 0.9032 (p0) cc_final: 0.8606 (p0) REVERT: D 252 ASP cc_start: 0.8612 (m-30) cc_final: 0.8230 (t0) REVERT: D 275 ILE cc_start: 0.9040 (mm) cc_final: 0.8767 (tp) REVERT: E 32 TYR cc_start: 0.8735 (m-80) cc_final: 0.8317 (m-80) REVERT: E 60 TYR cc_start: 0.9117 (m-80) cc_final: 0.8901 (m-10) REVERT: E 74 ASN cc_start: 0.6160 (m-40) cc_final: 0.5705 (m-40) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.1911 time to fit residues: 50.7905 Evaluate side-chains 150 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7376 Z= 0.298 Angle : 0.606 7.817 10082 Z= 0.321 Chirality : 0.044 0.190 1198 Planarity : 0.005 0.053 1283 Dihedral : 5.119 49.341 1084 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.45 (0.27), residues: 981 helix: 1.38 (0.27), residues: 377 sheet: -1.47 (0.34), residues: 213 loop : -1.22 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 332 HIS 0.007 0.002 HIS B 311 PHE 0.029 0.002 PHE E 68 TYR 0.027 0.002 TYR B 59 ARG 0.005 0.001 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LEU cc_start: 0.7377 (mt) cc_final: 0.7108 (pp) REVERT: A 140 MET cc_start: 0.7454 (mmt) cc_final: 0.7086 (mmt) REVERT: A 145 ASN cc_start: 0.7542 (t0) cc_final: 0.6724 (p0) REVERT: A 174 MET cc_start: 0.8589 (mmm) cc_final: 0.8282 (tpp) REVERT: A 177 MET cc_start: 0.8582 (mmm) cc_final: 0.8293 (mmm) REVERT: A 276 LEU cc_start: 0.9004 (tp) cc_final: 0.8693 (tp) REVERT: B 46 ARG cc_start: 0.8426 (mtt180) cc_final: 0.7407 (mmp-170) REVERT: B 111 TYR cc_start: 0.8647 (m-80) cc_final: 0.8124 (m-80) REVERT: B 188 MET cc_start: 0.8932 (mmm) cc_final: 0.8661 (mmm) REVERT: B 262 MET cc_start: 0.8523 (tpp) cc_final: 0.8226 (tpp) REVERT: B 290 ASP cc_start: 0.6923 (m-30) cc_final: 0.6721 (m-30) REVERT: B 291 ASP cc_start: 0.7890 (t70) cc_final: 0.7377 (m-30) REVERT: D 17 LYS cc_start: 0.9210 (ttmt) cc_final: 0.8791 (tppt) REVERT: D 217 VAL cc_start: 0.8151 (t) cc_final: 0.7927 (p) REVERT: D 220 HIS cc_start: 0.7230 (t70) cc_final: 0.6925 (m170) REVERT: D 222 PHE cc_start: 0.6743 (t80) cc_final: 0.5989 (t80) REVERT: D 233 LYS cc_start: 0.9246 (mmmt) cc_final: 0.8811 (mmtt) REVERT: D 239 ASN cc_start: 0.9039 (p0) cc_final: 0.8728 (p0) REVERT: D 252 ASP cc_start: 0.8609 (m-30) cc_final: 0.8131 (t0) REVERT: E 60 TYR cc_start: 0.9200 (m-80) cc_final: 0.8928 (m-10) REVERT: E 72 ARG cc_start: 0.8199 (ptm-80) cc_final: 0.7782 (mtm110) REVERT: E 74 ASN cc_start: 0.6193 (m-40) cc_final: 0.5470 (p0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1591 time to fit residues: 40.9301 Evaluate side-chains 143 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 55 optimal weight: 0.0020 chunk 23 optimal weight: 0.1980 chunk 93 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 0.0370 chunk 90 optimal weight: 2.9990 overall best weight: 1.2470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN E 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7376 Z= 0.204 Angle : 0.548 7.347 10082 Z= 0.289 Chirality : 0.042 0.169 1198 Planarity : 0.004 0.045 1283 Dihedral : 5.047 59.994 1084 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.25 (0.27), residues: 981 helix: 1.55 (0.27), residues: 380 sheet: -1.44 (0.33), residues: 213 loop : -1.08 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 332 HIS 0.005 0.001 HIS D 347 PHE 0.024 0.002 PHE B 292 TYR 0.020 0.001 TYR B 59 ARG 0.009 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LEU cc_start: 0.7299 (mt) cc_final: 0.7020 (pp) REVERT: A 140 MET cc_start: 0.7460 (mmt) cc_final: 0.6990 (mmt) REVERT: A 145 ASN cc_start: 0.7543 (t0) cc_final: 0.6737 (p0) REVERT: A 174 MET cc_start: 0.8797 (mmm) cc_final: 0.8447 (tpp) REVERT: A 177 MET cc_start: 0.8391 (mmm) cc_final: 0.8040 (mmm) REVERT: A 241 LEU cc_start: 0.7729 (mp) cc_final: 0.7458 (mp) REVERT: B 43 ILE cc_start: 0.7326 (tp) cc_final: 0.6882 (mm) REVERT: B 46 ARG cc_start: 0.8447 (mtt180) cc_final: 0.7527 (mmp-170) REVERT: B 111 TYR cc_start: 0.8563 (m-80) cc_final: 0.8090 (m-80) REVERT: B 188 MET cc_start: 0.8891 (mmm) cc_final: 0.8658 (mmm) REVERT: B 230 ASN cc_start: 0.8120 (m-40) cc_final: 0.7886 (m110) REVERT: B 262 MET cc_start: 0.8480 (tpp) cc_final: 0.8073 (tpp) REVERT: B 291 ASP cc_start: 0.7769 (t70) cc_final: 0.7313 (m-30) REVERT: B 332 TRP cc_start: 0.8880 (m-10) cc_final: 0.8558 (m-10) REVERT: D 17 LYS cc_start: 0.9194 (ttmt) cc_final: 0.8804 (tppt) REVERT: D 217 VAL cc_start: 0.7991 (t) cc_final: 0.7769 (p) REVERT: D 220 HIS cc_start: 0.7231 (t70) cc_final: 0.6936 (m170) REVERT: D 233 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8733 (mmtt) REVERT: D 239 ASN cc_start: 0.8932 (p0) cc_final: 0.8524 (p0) REVERT: D 252 ASP cc_start: 0.8452 (m-30) cc_final: 0.8069 (t0) REVERT: D 265 SER cc_start: 0.8910 (m) cc_final: 0.8575 (t) REVERT: E 60 TYR cc_start: 0.9181 (m-80) cc_final: 0.8833 (m-10) REVERT: E 68 PHE cc_start: 0.7552 (m-80) cc_final: 0.7179 (m-80) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1684 time to fit residues: 44.6262 Evaluate side-chains 156 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.0370 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 79 optimal weight: 0.1980 chunk 52 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7376 Z= 0.279 Angle : 0.584 7.953 10082 Z= 0.310 Chirality : 0.043 0.179 1198 Planarity : 0.005 0.054 1283 Dihedral : 5.036 51.211 1084 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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 (0.27), residues: 981 helix: 1.46 (0.27), residues: 379 sheet: -1.45 (0.33), residues: 223 loop : -0.96 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 332 HIS 0.006 0.001 HIS D 347 PHE 0.020 0.002 PHE A 182 TYR 0.024 0.002 TYR B 59 ARG 0.007 0.001 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LEU cc_start: 0.7518 (mt) cc_final: 0.7132 (pp) REVERT: A 140 MET cc_start: 0.7372 (mmt) cc_final: 0.7044 (mmt) REVERT: A 145 ASN cc_start: 0.7532 (t0) cc_final: 0.6677 (p0) REVERT: A 174 MET cc_start: 0.8573 (mmm) cc_final: 0.8295 (tpp) REVERT: A 241 LEU cc_start: 0.7739 (mp) cc_final: 0.7391 (mp) REVERT: A 245 CYS cc_start: 0.9107 (m) cc_final: 0.8892 (m) REVERT: A 290 TYR cc_start: 0.8814 (t80) cc_final: 0.8599 (t80) REVERT: B 46 ARG cc_start: 0.8419 (mtt180) cc_final: 0.7308 (mmp-170) REVERT: B 111 TYR cc_start: 0.8605 (m-80) cc_final: 0.8124 (m-80) REVERT: B 230 ASN cc_start: 0.8278 (m-40) cc_final: 0.7926 (m110) REVERT: B 262 MET cc_start: 0.8508 (tpp) cc_final: 0.8063 (tpp) REVERT: B 290 ASP cc_start: 0.6671 (m-30) cc_final: 0.6445 (m-30) REVERT: B 291 ASP cc_start: 0.7792 (t70) cc_final: 0.7233 (m-30) REVERT: B 332 TRP cc_start: 0.8995 (m-10) cc_final: 0.8742 (m-10) REVERT: D 17 LYS cc_start: 0.9189 (ttmt) cc_final: 0.8782 (tppt) REVERT: D 220 HIS cc_start: 0.7214 (t70) cc_final: 0.6978 (m170) REVERT: D 233 LYS cc_start: 0.9210 (mmmt) cc_final: 0.8804 (mmtt) REVERT: D 252 ASP cc_start: 0.8521 (m-30) cc_final: 0.8118 (t0) REVERT: D 255 ARG cc_start: 0.7890 (mtp-110) cc_final: 0.7045 (mmm-85) REVERT: D 265 SER cc_start: 0.8960 (m) cc_final: 0.8640 (t) REVERT: E 60 TYR cc_start: 0.9208 (m-80) cc_final: 0.8916 (m-10) REVERT: E 68 PHE cc_start: 0.7619 (m-80) cc_final: 0.7205 (m-80) REVERT: E 81 LEU cc_start: 0.8416 (tp) cc_final: 0.8210 (tp) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1713 time to fit residues: 43.1530 Evaluate side-chains 151 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 59 optimal weight: 0.0020 chunk 63 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 81 optimal weight: 0.3980 overall best weight: 1.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN D 19 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7376 Z= 0.232 Angle : 0.562 7.188 10082 Z= 0.295 Chirality : 0.042 0.189 1198 Planarity : 0.004 0.053 1283 Dihedral : 4.905 44.824 1084 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.16 (0.27), residues: 981 helix: 1.52 (0.27), residues: 382 sheet: -1.28 (0.33), residues: 224 loop : -0.97 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 332 HIS 0.005 0.001 HIS D 347 PHE 0.020 0.002 PHE A 182 TYR 0.018 0.001 TYR B 59 ARG 0.008 0.001 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LEU cc_start: 0.7622 (mt) cc_final: 0.7254 (pp) REVERT: A 140 MET cc_start: 0.7471 (mmt) cc_final: 0.6966 (mmt) REVERT: A 145 ASN cc_start: 0.7663 (t0) cc_final: 0.6715 (p0) REVERT: A 174 MET cc_start: 0.8816 (mmm) cc_final: 0.8474 (tpp) REVERT: A 177 MET cc_start: 0.8498 (mmm) cc_final: 0.8026 (mmm) REVERT: A 193 MET cc_start: 0.7682 (mtm) cc_final: 0.7444 (mtp) REVERT: A 245 CYS cc_start: 0.9116 (m) cc_final: 0.8840 (m) REVERT: A 290 TYR cc_start: 0.8874 (t80) cc_final: 0.8649 (t80) REVERT: B 46 ARG cc_start: 0.8492 (mtt180) cc_final: 0.7533 (mmp-170) REVERT: B 111 TYR cc_start: 0.8586 (m-80) cc_final: 0.8121 (m-80) REVERT: B 230 ASN cc_start: 0.8375 (m-40) cc_final: 0.8019 (m110) REVERT: B 262 MET cc_start: 0.8478 (tpp) cc_final: 0.8028 (tpp) REVERT: B 290 ASP cc_start: 0.6673 (m-30) cc_final: 0.6450 (m-30) REVERT: B 291 ASP cc_start: 0.7764 (t70) cc_final: 0.7228 (m-30) REVERT: B 332 TRP cc_start: 0.8976 (m-10) cc_final: 0.8747 (m-10) REVERT: D 17 LYS cc_start: 0.9160 (ttmt) cc_final: 0.8775 (tppt) REVERT: D 220 HIS cc_start: 0.7128 (t70) cc_final: 0.6910 (m170) REVERT: D 233 LYS cc_start: 0.9182 (mmmt) cc_final: 0.8771 (mmtt) REVERT: D 252 ASP cc_start: 0.8504 (m-30) cc_final: 0.8145 (t0) REVERT: D 265 SER cc_start: 0.8899 (m) cc_final: 0.8591 (t) REVERT: D 273 ARG cc_start: 0.8125 (ptp-110) cc_final: 0.7670 (mtt180) REVERT: D 276 SER cc_start: 0.8819 (m) cc_final: 0.8079 (p) REVERT: E 58 ILE cc_start: 0.8760 (mt) cc_final: 0.8470 (tt) REVERT: E 68 PHE cc_start: 0.7457 (m-80) cc_final: 0.7082 (m-80) REVERT: E 81 LEU cc_start: 0.8421 (tp) cc_final: 0.8218 (tp) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1727 time to fit residues: 43.1644 Evaluate side-chains 156 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 50.0000 chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN E 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7376 Z= 0.185 Angle : 0.544 6.830 10082 Z= 0.286 Chirality : 0.043 0.209 1198 Planarity : 0.004 0.049 1283 Dihedral : 4.758 39.147 1084 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.02 (0.27), residues: 981 helix: 1.67 (0.27), residues: 381 sheet: -1.15 (0.33), residues: 222 loop : -0.96 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.004 0.001 HIS D 347 PHE 0.027 0.002 PHE D 330 TYR 0.013 0.001 TYR B 59 ARG 0.008 0.001 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.7990 (tt) cc_final: 0.7439 (pp) REVERT: A 137 LEU cc_start: 0.7438 (mt) cc_final: 0.7073 (pp) REVERT: A 140 MET cc_start: 0.7497 (mmt) cc_final: 0.7056 (mmt) REVERT: A 145 ASN cc_start: 0.7666 (t0) cc_final: 0.6695 (p0) REVERT: A 177 MET cc_start: 0.8554 (mmm) cc_final: 0.8071 (mmm) REVERT: A 193 MET cc_start: 0.7556 (mtm) cc_final: 0.7308 (mtp) REVERT: A 241 LEU cc_start: 0.7675 (mp) cc_final: 0.7264 (mp) REVERT: A 245 CYS cc_start: 0.9112 (m) cc_final: 0.8820 (m) REVERT: A 290 TYR cc_start: 0.8860 (t80) cc_final: 0.8632 (t80) REVERT: B 46 ARG cc_start: 0.8241 (mtt180) cc_final: 0.7408 (mmp-170) REVERT: B 111 TYR cc_start: 0.8552 (m-80) cc_final: 0.8109 (m-80) REVERT: B 230 ASN cc_start: 0.8313 (m-40) cc_final: 0.7978 (m110) REVERT: B 262 MET cc_start: 0.8481 (tpp) cc_final: 0.8007 (tpp) REVERT: B 290 ASP cc_start: 0.6180 (m-30) cc_final: 0.5907 (m-30) REVERT: B 291 ASP cc_start: 0.7384 (t70) cc_final: 0.6848 (m-30) REVERT: B 332 TRP cc_start: 0.8957 (m-10) cc_final: 0.8709 (m-10) REVERT: D 17 LYS cc_start: 0.9122 (ttmt) cc_final: 0.8737 (tppt) REVERT: D 239 ASN cc_start: 0.8902 (p0) cc_final: 0.8702 (p0) REVERT: D 252 ASP cc_start: 0.8681 (m-30) cc_final: 0.8457 (t0) REVERT: D 265 SER cc_start: 0.8934 (m) cc_final: 0.8631 (t) REVERT: D 273 ARG cc_start: 0.8064 (ptp-110) cc_final: 0.7606 (mtt180) REVERT: D 276 SER cc_start: 0.8774 (m) cc_final: 0.8061 (p) REVERT: E 58 ILE cc_start: 0.8728 (mt) cc_final: 0.8465 (tt) REVERT: E 68 PHE cc_start: 0.7326 (m-80) cc_final: 0.6996 (m-80) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1726 time to fit residues: 44.7078 Evaluate side-chains 158 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN D 236 GLN E 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7376 Z= 0.279 Angle : 0.612 7.822 10082 Z= 0.321 Chirality : 0.044 0.193 1198 Planarity : 0.004 0.049 1283 Dihedral : 5.116 39.760 1084 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -0.12 (0.27), residues: 981 helix: 1.52 (0.27), residues: 378 sheet: -1.09 (0.34), residues: 222 loop : -1.00 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 36 HIS 0.005 0.001 HIS D 347 PHE 0.023 0.002 PHE B 292 TYR 0.020 0.002 TYR B 59 ARG 0.005 0.001 ARG A 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 LEU cc_start: 0.7678 (mt) cc_final: 0.7280 (pp) REVERT: A 140 MET cc_start: 0.7220 (mmt) cc_final: 0.6841 (mmt) REVERT: A 145 ASN cc_start: 0.7620 (t0) cc_final: 0.6675 (p0) REVERT: A 177 MET cc_start: 0.8487 (mmm) cc_final: 0.8057 (mmm) REVERT: A 241 LEU cc_start: 0.7790 (mp) cc_final: 0.7373 (mp) REVERT: A 245 CYS cc_start: 0.8993 (m) cc_final: 0.8677 (m) REVERT: A 290 TYR cc_start: 0.8914 (t80) cc_final: 0.8679 (t80) REVERT: B 46 ARG cc_start: 0.8453 (mtt180) cc_final: 0.7585 (mmp-170) REVERT: B 111 TYR cc_start: 0.8688 (m-80) cc_final: 0.8224 (m-80) REVERT: B 230 ASN cc_start: 0.8260 (m-40) cc_final: 0.8053 (m110) REVERT: B 262 MET cc_start: 0.8505 (tpp) cc_final: 0.8008 (tpp) REVERT: B 290 ASP cc_start: 0.6505 (m-30) cc_final: 0.6215 (m-30) REVERT: B 291 ASP cc_start: 0.7460 (t70) cc_final: 0.6921 (m-30) REVERT: B 332 TRP cc_start: 0.9148 (m-10) cc_final: 0.8711 (m-10) REVERT: D 17 LYS cc_start: 0.9137 (ttmt) cc_final: 0.8768 (tppt) REVERT: D 252 ASP cc_start: 0.8771 (m-30) cc_final: 0.8492 (t0) REVERT: D 265 SER cc_start: 0.8985 (m) cc_final: 0.8707 (t) REVERT: D 276 SER cc_start: 0.8877 (m) cc_final: 0.8132 (p) REVERT: E 58 ILE cc_start: 0.8858 (mt) cc_final: 0.8612 (tt) REVERT: E 68 PHE cc_start: 0.7535 (m-80) cc_final: 0.7130 (m-80) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1679 time to fit residues: 42.1014 Evaluate side-chains 145 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN D 220 HIS D 236 GLN E 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.132176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117686 restraints weight = 14884.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119467 restraints weight = 10009.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.120638 restraints weight = 7501.703| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7376 Z= 0.234 Angle : 0.584 9.397 10082 Z= 0.305 Chirality : 0.043 0.178 1198 Planarity : 0.004 0.047 1283 Dihedral : 4.880 34.334 1084 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.27), residues: 981 helix: 1.62 (0.27), residues: 373 sheet: -1.00 (0.35), residues: 214 loop : -1.06 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.010 0.001 HIS D 220 PHE 0.022 0.002 PHE D 330 TYR 0.014 0.001 TYR B 59 ARG 0.004 0.001 ARG D 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1835.55 seconds wall clock time: 34 minutes 15.69 seconds (2055.69 seconds total)