Starting phenix.real_space_refine on Sat Dec 9 11:20:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y67_33636/12_2023/7y67_33636_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y67_33636/12_2023/7y67_33636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y67_33636/12_2023/7y67_33636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y67_33636/12_2023/7y67_33636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y67_33636/12_2023/7y67_33636_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y67_33636/12_2023/7y67_33636_neut_updated.pdb" } resolution = 2.8 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2047 atoms to isotropic. 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 59 5.16 5 C 5675 2.51 5 N 1514 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "D ARG 175": "NH1" <-> "NH2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S GLU 153": "OE1" <-> "OE2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" 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: 8889 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1803 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2197 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 1 Chain: "S" 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: "L" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 65 Classifications: {'peptide': 6} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'ZAL:plan-1': 1, 'MEA:plan-2': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 5.17, per 1000 atoms: 0.58 Number of scatterers: 8889 At special positions: 0 Unit cell: (95.2, 123.25, 132.6, 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 59 16.00 O 1641 8.00 N 1514 7.00 C 5675 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 188 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 3.49 Conformation dependent library (CDL) restraints added in 1.9 seconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAR L 6 " Input volumes are d-peptide like pdb=" CB ZAL L 4 " Number of C-beta restraints generated: 2120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 13 sheets defined 33.8% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 removed outlier: 4.260A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.082A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.736A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 7 through 22 Processing helix chain 'C' and resid 30 through 47 removed outlier: 5.014A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLU C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'D' and resid 35 through 64 removed outlier: 3.699A pdb=" N LEU D 39 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 87 removed outlier: 4.077A pdb=" N TRP D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 78 " --> pdb=" O TRP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 106 through 109 No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 112 through 115 No H-bonds generated for 'chain 'D' and resid 112 through 115' Processing helix chain 'D' and resid 118 through 138 removed outlier: 4.258A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 150 through 173 removed outlier: 3.731A pdb=" N ALA D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D 165 " --> pdb=" O TRP D 161 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Proline residue: D 170 - end of helix Processing helix chain 'D' and resid 197 through 230 Proline residue: D 214 - end of helix Processing helix chain 'D' and resid 239 through 267 Proline residue: D 257 - end of helix removed outlier: 3.591A pdb=" N MET D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 288 removed outlier: 4.560A pdb=" N SER D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 302 Proline residue: D 297 - end of helix removed outlier: 3.933A pdb=" N TYR D 300 " --> pdb=" O ASN D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 313 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.846A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.875A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.573A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.699A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.897A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.958A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.551A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.780A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 175 through 178 Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 114 through 117 removed outlier: 3.596A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 146 through 148 removed outlier: 7.236A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 155 through 160 375 hydrogen bonds defined for protein. 1086 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: 2.52 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2859 1.35 - 1.47: 2244 1.47 - 1.58: 3891 1.58 - 1.70: 1 1.70 - 1.82: 83 Bond restraints: 9078 Sorted by residual: bond pdb=" C MEA L 1 " pdb=" N LYS L 2 " ideal model delta sigma weight residual 1.329 1.390 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" N ARG A 208 " pdb=" CA ARG A 208 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.30e-02 5.92e+03 7.66e+00 bond pdb=" CB PRO S 75 " pdb=" CG PRO S 75 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.39e+00 bond pdb=" CE1 HIS D 100 " pdb=" NE2 HIS D 100 " ideal model delta sigma weight residual 1.321 1.338 -0.017 1.00e-02 1.00e+04 2.81e+00 bond pdb=" N LYS D 279 " pdb=" CA LYS D 279 " ideal model delta sigma weight residual 1.458 1.479 -0.021 1.30e-02 5.92e+03 2.60e+00 ... (remaining 9073 not shown) Histogram of bond angle deviations from ideal: 98.27 - 107.19: 222 107.19 - 116.12: 5799 116.12 - 125.05: 6124 125.05 - 133.98: 151 133.98 - 142.91: 6 Bond angle restraints: 12302 Sorted by residual: angle pdb=" O MEA L 1 " pdb=" C MEA L 1 " pdb=" N LYS L 2 " ideal model delta sigma weight residual 123.00 99.93 23.07 1.60e+00 3.91e-01 2.08e+02 angle pdb=" CA MEA L 1 " pdb=" C MEA L 1 " pdb=" N LYS L 2 " ideal model delta sigma weight residual 116.20 140.52 -24.32 2.00e+00 2.50e-01 1.48e+02 angle pdb=" C MEA L 1 " pdb=" N LYS L 2 " pdb=" CA LYS L 2 " ideal model delta sigma weight residual 121.70 142.91 -21.21 1.80e+00 3.09e-01 1.39e+02 angle pdb=" CA PRO S 75 " pdb=" N PRO S 75 " pdb=" CD PRO S 75 " ideal model delta sigma weight residual 112.00 104.63 7.37 1.40e+00 5.10e-01 2.77e+01 angle pdb=" N LYS D 279 " pdb=" CA LYS D 279 " pdb=" C LYS D 279 " ideal model delta sigma weight residual 112.23 106.24 5.99 1.26e+00 6.30e-01 2.26e+01 ... (remaining 12297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.34: 5131 25.34 - 50.67: 218 50.67 - 76.01: 14 76.01 - 101.35: 5 101.35 - 126.68: 1 Dihedral angle restraints: 5369 sinusoidal: 2086 harmonic: 3283 Sorted by residual: dihedral pdb=" CD DAR L 6 " pdb=" NE DAR L 6 " pdb=" CZ DAR L 6 " pdb=" NH1 DAR L 6 " ideal model delta sinusoidal sigma weight residual 0.00 -126.68 126.68 1 1.00e+01 1.00e-02 1.53e+02 dihedral pdb=" CA ZAL L 4 " pdb=" C ZAL L 4 " pdb=" N TRP L 5 " pdb=" CA TRP L 5 " ideal model delta harmonic sigma weight residual 180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA TRP B 297 " pdb=" C TRP B 297 " pdb=" N ASP B 298 " pdb=" CA ASP B 298 " ideal model delta harmonic sigma weight residual 180.00 163.00 17.00 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 5366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 853 0.030 - 0.059: 338 0.059 - 0.089: 128 0.089 - 0.119: 67 0.119 - 0.148: 16 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CA HIS D 100 " pdb=" N HIS D 100 " pdb=" C HIS D 100 " pdb=" CB HIS D 100 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" C1 ZAL L 4 " pdb=" CB ZAL L 4 " pdb=" C2 ZAL L 4 " pdb=" C6 ZAL L 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 1399 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD DAR L 6 " -0.905 9.50e-02 1.11e+02 4.06e-01 9.95e+01 pdb=" NE DAR L 6 " 0.052 2.00e-02 2.50e+03 pdb=" CZ DAR L 6 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 DAR L 6 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 DAR L 6 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.078 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO S 75 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MEA L 1 " -0.022 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C MEA L 1 " 0.060 2.00e-02 2.50e+03 pdb=" O MEA L 1 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS L 2 " -0.021 2.00e-02 2.50e+03 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 26 2.48 - 3.09: 5768 3.09 - 3.69: 12589 3.69 - 4.30: 18129 4.30 - 4.90: 30978 Nonbonded interactions: 67490 Sorted by model distance: nonbonded pdb=" O THR A 327 " pdb=" OD1 ASP A 328 " model vdw 1.877 3.040 nonbonded pdb=" O ZAL L 4 " pdb=" O TRP L 5 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.227 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.258 2.440 nonbonded pdb=" OE2 GLU A 207 " pdb=" NZ LYS A 209 " model vdw 2.259 2.520 ... (remaining 67485 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 3.910 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.520 Find NCS groups from input model: 0.250 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 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 : 0.003 0.105 9078 Z= 0.190 Angle : 0.691 24.323 12302 Z= 0.388 Chirality : 0.042 0.148 1402 Planarity : 0.011 0.406 1549 Dihedral : 13.094 126.683 3243 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.10 % Allowed : 0.21 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.59 (0.25), residues: 1114 helix: 2.03 (0.28), residues: 367 sheet: 0.71 (0.31), residues: 296 loop : -1.25 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 5 HIS 0.004 0.001 HIS A 188 PHE 0.017 0.001 PHE S 177 TYR 0.018 0.001 TYR D 300 ARG 0.007 0.000 ARG D 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.160 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 1.1224 time to fit residues: 257.0387 Evaluate side-chains 172 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.999 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.3980 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 125 ASN B 340 ASN C 44 HIS C 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9078 Z= 0.158 Angle : 0.510 6.224 12302 Z= 0.265 Chirality : 0.041 0.137 1402 Planarity : 0.003 0.064 1549 Dihedral : 6.830 179.216 1236 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.18 % Allowed : 13.10 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.60 (0.25), residues: 1114 helix: 2.03 (0.27), residues: 372 sheet: 0.69 (0.31), residues: 290 loop : -1.23 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.006 0.001 HIS A 188 PHE 0.016 0.001 PHE A 189 TYR 0.008 0.001 TYR S 190 ARG 0.007 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 1.173 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 182 average time/residue: 1.1894 time to fit residues: 231.0296 Evaluate side-chains 180 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 3 average time/residue: 0.8086 time to fit residues: 3.9931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.0370 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 54 HIS B 75 GLN B 125 ASN B 237 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN S 35 HIS S 186 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9078 Z= 0.280 Angle : 0.580 7.097 12302 Z= 0.305 Chirality : 0.043 0.133 1402 Planarity : 0.004 0.053 1549 Dihedral : 6.796 175.904 1236 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.22 % Allowed : 15.38 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.38 (0.25), residues: 1114 helix: 1.84 (0.27), residues: 373 sheet: 0.61 (0.31), residues: 296 loop : -1.42 (0.24), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 47 HIS 0.006 0.002 HIS B 62 PHE 0.019 0.002 PHE A 189 TYR 0.022 0.002 TYR D 300 ARG 0.007 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 0.850 Fit side-chains outliers start: 31 outliers final: 17 residues processed: 200 average time/residue: 1.1586 time to fit residues: 247.4895 Evaluate side-chains 191 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 174 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 9 residues processed: 8 average time/residue: 0.5994 time to fit residues: 6.7256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 88 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9078 Z= 0.294 Angle : 0.591 7.699 12302 Z= 0.311 Chirality : 0.043 0.132 1402 Planarity : 0.004 0.048 1549 Dihedral : 6.791 176.533 1236 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.22 % Allowed : 19.65 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.33 (0.24), residues: 1114 helix: 1.86 (0.27), residues: 374 sheet: 0.54 (0.31), residues: 296 loop : -1.49 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP S 47 HIS 0.006 0.002 HIS B 54 PHE 0.018 0.002 PHE A 189 TYR 0.018 0.002 TYR D 300 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 1.017 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 201 average time/residue: 1.1665 time to fit residues: 250.5819 Evaluate side-chains 193 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 179 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.1324 time to fit residues: 2.1666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9078 Z= 0.250 Angle : 0.560 10.148 12302 Z= 0.295 Chirality : 0.042 0.136 1402 Planarity : 0.004 0.045 1549 Dihedral : 6.760 178.485 1236 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.74 % Allowed : 20.79 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.31 (0.25), residues: 1114 helix: 1.81 (0.27), residues: 378 sheet: 0.47 (0.31), residues: 302 loop : -1.46 (0.24), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 176 HIS 0.004 0.001 HIS S 167 PHE 0.017 0.002 PHE A 189 TYR 0.016 0.002 TYR D 300 ARG 0.008 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 177 time to evaluate : 1.032 Fit side-chains outliers start: 36 outliers final: 23 residues processed: 195 average time/residue: 1.1831 time to fit residues: 246.1564 Evaluate side-chains 197 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 13 residues processed: 11 average time/residue: 0.3846 time to fit residues: 6.2373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 40.0000 chunk 103 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN C 59 ASN D 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9078 Z= 0.177 Angle : 0.533 13.632 12302 Z= 0.277 Chirality : 0.041 0.136 1402 Planarity : 0.003 0.043 1549 Dihedral : 6.682 179.053 1236 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.01 % Allowed : 21.73 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.45 (0.25), residues: 1114 helix: 1.95 (0.27), residues: 378 sheet: 0.65 (0.32), residues: 289 loop : -1.46 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 176 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE A 189 TYR 0.014 0.001 TYR D 300 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 1.015 Fit side-chains outliers start: 29 outliers final: 21 residues processed: 192 average time/residue: 1.2864 time to fit residues: 263.9362 Evaluate side-chains 199 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 8 average time/residue: 0.3477 time to fit residues: 4.8812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN D 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9078 Z= 0.258 Angle : 0.574 13.293 12302 Z= 0.299 Chirality : 0.042 0.134 1402 Planarity : 0.004 0.042 1549 Dihedral : 6.758 179.913 1236 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.81 % Allowed : 22.66 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.39 (0.25), residues: 1114 helix: 1.94 (0.27), residues: 373 sheet: 0.55 (0.31), residues: 302 loop : -1.49 (0.25), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP S 47 HIS 0.004 0.001 HIS S 167 PHE 0.016 0.002 PHE A 189 TYR 0.014 0.002 TYR S 228 ARG 0.004 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 177 time to evaluate : 1.076 Fit side-chains outliers start: 27 outliers final: 17 residues processed: 192 average time/residue: 1.2014 time to fit residues: 246.3715 Evaluate side-chains 190 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 6 average time/residue: 0.3937 time to fit residues: 4.1615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 102 optimal weight: 0.3980 chunk 93 optimal weight: 0.4980 chunk 99 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9078 Z= 0.152 Angle : 0.517 14.246 12302 Z= 0.265 Chirality : 0.040 0.140 1402 Planarity : 0.003 0.041 1549 Dihedral : 6.581 179.867 1236 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.70 % Allowed : 22.97 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.49 (0.25), residues: 1114 helix: 2.05 (0.28), residues: 376 sheet: 0.66 (0.32), residues: 279 loop : -1.42 (0.24), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 176 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE A 189 TYR 0.012 0.001 TYR D 300 ARG 0.002 0.000 ARG S 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 171 time to evaluate : 1.012 Fit side-chains outliers start: 26 outliers final: 16 residues processed: 191 average time/residue: 1.2160 time to fit residues: 247.4502 Evaluate side-chains 186 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.8220 time to fit residues: 4.3312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN B 340 ASN C 59 ASN D 145 GLN S 35 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9078 Z= 0.212 Angle : 0.551 13.744 12302 Z= 0.285 Chirality : 0.041 0.145 1402 Planarity : 0.003 0.040 1549 Dihedral : 6.655 179.707 1236 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.18 % Allowed : 23.80 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.42 (0.25), residues: 1114 helix: 1.96 (0.27), residues: 379 sheet: 0.59 (0.32), residues: 276 loop : -1.42 (0.24), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 176 HIS 0.004 0.001 HIS S 167 PHE 0.017 0.002 PHE A 189 TYR 0.013 0.002 TYR D 258 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 1.066 Fit side-chains outliers start: 21 outliers final: 15 residues processed: 187 average time/residue: 1.2560 time to fit residues: 250.2032 Evaluate side-chains 182 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 167 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.2098 time to fit residues: 1.6004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 0.0170 chunk 88 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.0010 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN D 145 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9078 Z= 0.142 Angle : 0.521 14.238 12302 Z= 0.267 Chirality : 0.040 0.141 1402 Planarity : 0.003 0.040 1549 Dihedral : 6.527 179.897 1236 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.87 % Allowed : 24.32 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.57 (0.25), residues: 1114 helix: 2.08 (0.27), residues: 379 sheet: 0.69 (0.32), residues: 278 loop : -1.34 (0.24), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 176 HIS 0.003 0.001 HIS B 54 PHE 0.014 0.001 PHE A 189 TYR 0.013 0.001 TYR D 258 ARG 0.010 0.000 ARG A 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 1.019 Fit side-chains outliers start: 18 outliers final: 15 residues processed: 186 average time/residue: 1.1400 time to fit residues: 226.7477 Evaluate side-chains 183 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 168 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.1499 time to fit residues: 1.8353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 125 ASN B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.128309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.106643 restraints weight = 12970.729| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.00 r_work: 0.3306 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9078 Z= 0.227 Angle : 0.564 13.953 12302 Z= 0.292 Chirality : 0.042 0.139 1402 Planarity : 0.004 0.039 1549 Dihedral : 6.651 179.625 1236 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.29 % Allowed : 23.91 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.44 (0.25), residues: 1114 helix: 1.98 (0.27), residues: 379 sheet: 0.59 (0.32), residues: 280 loop : -1.41 (0.24), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 176 HIS 0.004 0.001 HIS S 167 PHE 0.017 0.002 PHE A 189 TYR 0.020 0.002 TYR S 227 ARG 0.009 0.000 ARG A 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4194.33 seconds wall clock time: 74 minutes 42.73 seconds (4482.73 seconds total)