Starting phenix.real_space_refine on Wed Feb 14 05:07:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia2_35292/02_2024/8ia2_35292.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia2_35292/02_2024/8ia2_35292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia2_35292/02_2024/8ia2_35292.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia2_35292/02_2024/8ia2_35292.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia2_35292/02_2024/8ia2_35292.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia2_35292/02_2024/8ia2_35292.pdb" } resolution = 3.21 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= 0.004 sd= 0.020 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 54 5.16 5 C 5512 2.51 5 N 1486 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 24": "OD1" <-> "OD2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B ASP 299": "OD1" <-> "OD2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 220": "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: 8653 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2237 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 14, 'TRANS': 279} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 489 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1497 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 44} Link IDs: {'PTRANS': 4, 'TRANS': 204} Chain breaks: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 90 Chain: "C" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2435 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 8, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 110 Chain: "G" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 382 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1613 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 94 Time building chain proxies: 5.30, per 1000 atoms: 0.61 Number of scatterers: 8653 At special positions: 0 Unit cell: (83.9849, 124.383, 144.582, 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 54 16.00 O 1601 8.00 N 1486 7.00 C 5512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 47 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 54 " distance=2.04 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 55 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 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: 3.42 Conformation dependent library (CDL) restraints added in 2.0 seconds 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 17 sheets defined 41.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 36 through 53 Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 72 through 88 Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 105 through 140 Proline residue: A 113 - end of helix removed outlier: 4.531A pdb=" N LEU A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.754A pdb=" N GLN A 145 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 174 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 198 through 230 removed outlier: 5.045A pdb=" N TRP A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Proline residue: A 214 - end of helix Processing helix chain 'A' and resid 238 through 268 removed outlier: 3.603A pdb=" N SER A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 271 through 304 removed outlier: 4.052A pdb=" N PHE A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N SER A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N CYS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 4.066A pdb=" N TYR A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 39 through 41 No H-bonds generated for 'chain 'D' and resid 39 through 41' Processing helix chain 'D' and resid 44 through 66 removed outlier: 4.244A pdb=" N SER D 66 " --> pdb=" O ARG D 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.756A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.905A pdb=" N GLY B 204 " --> pdb=" O ASP B 201 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN B 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 201 through 205' Processing helix chain 'B' and resid 208 through 217 removed outlier: 4.974A pdb=" N ILE B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N HIS B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 217 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 257 through 261 removed outlier: 3.600A pdb=" N ILE B 261 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 282 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 329 through 351 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 25 removed outlier: 4.059A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.510A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.523A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 179 Processing sheet with id=AA2, first strand: chain 'B' and resid 189 through 191 removed outlier: 6.093A pdb=" N VAL B 34 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE B 200 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 36 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 225 through 227 removed outlier: 6.530A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.755A pdb=" N LEU C 336 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 337 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.661A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.631A pdb=" N GLY C 115 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 146 through 153 removed outlier: 6.729A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.738A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.093A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.558A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'H' and resid 33 through 35 removed outlier: 3.595A pdb=" N HIS H 35 " --> pdb=" O VAL H 97 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AB6, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB7, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.732A pdb=" N VAL H 147 " --> pdb=" O GLU H 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'H' and resid 194 through 195 removed outlier: 6.688A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) 449 hydrogen bonds defined for protein. 1260 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: 3.14 Time building geometry restraints manager: 3.72 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: 2828 1.35 - 1.47: 2255 1.47 - 1.60: 3675 1.60 - 1.72: 0 1.72 - 1.84: 68 Bond restraints: 8826 Sorted by residual: bond pdb=" CA PRO C 94 " pdb=" CB PRO C 94 " ideal model delta sigma weight residual 1.533 1.489 0.045 1.42e-02 4.96e+03 9.87e+00 bond pdb=" N HIS A 194 " pdb=" CA HIS A 194 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.39e+00 bond pdb=" CA PRO G 60 " pdb=" CB PRO G 60 " ideal model delta sigma weight residual 1.534 1.496 0.038 1.49e-02 4.50e+03 6.50e+00 bond pdb=" N PHE A 172 " pdb=" CA PHE A 172 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.31e-02 5.83e+03 6.33e+00 bond pdb=" N ILE C 93 " pdb=" CA ILE C 93 " ideal model delta sigma weight residual 1.460 1.476 -0.017 7.50e-03 1.78e+04 5.05e+00 ... (remaining 8821 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.87: 200 106.87 - 113.66: 4921 113.66 - 120.44: 3347 120.44 - 127.23: 3481 127.23 - 134.01: 91 Bond angle restraints: 12040 Sorted by residual: angle pdb=" N PRO H 181 " pdb=" CA PRO H 181 " pdb=" CB PRO H 181 " ideal model delta sigma weight residual 103.31 109.24 -5.93 8.90e-01 1.26e+00 4.44e+01 angle pdb=" N ARG A 198 " pdb=" CA ARG A 198 " pdb=" C ARG A 198 " ideal model delta sigma weight residual 114.56 108.75 5.81 1.27e+00 6.20e-01 2.09e+01 angle pdb=" CA PHE A 172 " pdb=" CB PHE A 172 " pdb=" CG PHE A 172 " ideal model delta sigma weight residual 113.80 118.28 -4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" N PRO G 60 " pdb=" CA PRO G 60 " pdb=" CB PRO G 60 " ideal model delta sigma weight residual 103.51 107.75 -4.24 9.60e-01 1.09e+00 1.95e+01 angle pdb=" O ILE C 93 " pdb=" C ILE C 93 " pdb=" N PRO C 94 " ideal model delta sigma weight residual 121.57 125.21 -3.64 8.70e-01 1.32e+00 1.75e+01 ... (remaining 12035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4769 17.99 - 35.97: 326 35.97 - 53.96: 57 53.96 - 71.95: 5 71.95 - 89.94: 8 Dihedral angle restraints: 5165 sinusoidal: 1692 harmonic: 3473 Sorted by residual: dihedral pdb=" CA GLN A 145 " pdb=" C GLN A 145 " pdb=" N ASN A 146 " pdb=" CA ASN A 146 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA TRP C 82 " pdb=" C TRP C 82 " pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta harmonic sigma weight residual 180.00 154.91 25.09 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CB CYS D 34 " pdb=" SG CYS D 34 " pdb=" SG CYS D 55 " pdb=" CB CYS D 55 " ideal model delta sinusoidal sigma weight residual -86.00 -126.01 40.01 1 1.00e+01 1.00e-02 2.25e+01 ... (remaining 5162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1005 0.041 - 0.082: 320 0.082 - 0.123: 83 0.123 - 0.164: 22 0.164 - 0.205: 1 Chirality restraints: 1431 Sorted by residual: chirality pdb=" CA PRO H 181 " pdb=" N PRO H 181 " pdb=" C PRO H 181 " pdb=" CB PRO H 181 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE C 93 " pdb=" N ILE C 93 " pdb=" C ILE C 93 " pdb=" CB ILE C 93 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA ILE C 232 " pdb=" N ILE C 232 " pdb=" C ILE C 232 " pdb=" CB ILE C 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1428 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 59 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C ASN G 59 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN G 59 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO G 60 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 106 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO H 107 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO H 107 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 107 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 183 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.45e+00 pdb=" N PRO A 184 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 184 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 184 " 0.026 5.00e-02 4.00e+02 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 362 2.71 - 3.26: 9595 3.26 - 3.81: 13902 3.81 - 4.35: 17463 4.35 - 4.90: 29824 Nonbonded interactions: 71146 Sorted by model distance: nonbonded pdb=" N GLU H 220 " pdb=" OE1 GLU H 220 " model vdw 2.166 2.520 nonbonded pdb=" O GLN B 333 " pdb=" NE2 GLN B 333 " model vdw 2.202 2.520 nonbonded pdb=" N GLN D 3 " pdb=" OE1 GLN D 3 " model vdw 2.207 2.520 nonbonded pdb=" O VAL A 58 " pdb=" OG1 THR A 62 " model vdw 2.211 2.440 nonbonded pdb=" O SER A 237 " pdb=" OG1 THR A 238 " model vdw 2.213 2.440 ... (remaining 71141 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: 2.680 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.960 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 29.330 Find NCS groups from input model: 0.290 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8826 Z= 0.300 Angle : 0.761 7.695 12040 Z= 0.444 Chirality : 0.044 0.205 1431 Planarity : 0.005 0.050 1536 Dihedral : 13.187 89.935 2903 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.49 % Allowed : 9.59 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.23), residues: 1183 helix: -0.05 (0.24), residues: 410 sheet: -1.02 (0.29), residues: 284 loop : -1.02 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 82 HIS 0.009 0.002 HIS A 100 PHE 0.027 0.002 PHE B 192 TYR 0.021 0.003 TYR A 181 ARG 0.004 0.001 ARG C 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 115 LEU cc_start: 0.7672 (mm) cc_final: 0.7462 (mp) REVERT: A 195 ASP cc_start: 0.7413 (t0) cc_final: 0.7207 (t0) REVERT: A 282 ASP cc_start: 0.6941 (t70) cc_final: 0.6686 (t0) REVERT: B 208 GLU cc_start: 0.8070 (tt0) cc_final: 0.7813 (tt0) REVERT: B 309 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7055 (mt-10) REVERT: C 247 ASP cc_start: 0.7502 (t0) cc_final: 0.7282 (t0) REVERT: G 42 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7240 (mm-30) REVERT: H 6 GLU cc_start: 0.3203 (mt-10) cc_final: 0.2679 (mt-10) REVERT: H 55 SER cc_start: 0.7763 (m) cc_final: 0.7388 (p) outliers start: 4 outliers final: 3 residues processed: 144 average time/residue: 0.2221 time to fit residues: 43.6224 Evaluate side-chains 128 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain H residue 31 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 0.0000 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8826 Z= 0.263 Angle : 0.675 8.627 12040 Z= 0.351 Chirality : 0.045 0.152 1431 Planarity : 0.005 0.048 1536 Dihedral : 6.144 62.884 1279 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.18 % Allowed : 11.89 % Favored : 85.92 % 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: -0.64 (0.24), residues: 1183 helix: 0.55 (0.25), residues: 421 sheet: -1.01 (0.29), residues: 275 loop : -0.79 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 82 HIS 0.008 0.001 HIS A 100 PHE 0.021 0.002 PHE H 212 TYR 0.019 0.002 TYR A 181 ARG 0.003 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 0.979 Fit side-chains REVERT: A 195 ASP cc_start: 0.7490 (t0) cc_final: 0.7278 (t0) REVERT: A 282 ASP cc_start: 0.6912 (t70) cc_final: 0.6416 (t0) REVERT: C 234 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8705 (m-80) REVERT: G 42 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7337 (mm-30) REVERT: H 50 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.6748 (t80) REVERT: H 55 SER cc_start: 0.7856 (m) cc_final: 0.7477 (p) outliers start: 18 outliers final: 11 residues processed: 147 average time/residue: 0.2208 time to fit residues: 44.6275 Evaluate side-chains 139 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN D 71 GLN C 183 HIS C 230 ASN H 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 8826 Z= 0.526 Angle : 0.805 8.743 12040 Z= 0.420 Chirality : 0.050 0.162 1431 Planarity : 0.006 0.090 1536 Dihedral : 6.426 65.722 1278 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 4.85 % Allowed : 13.59 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.24), residues: 1183 helix: 0.16 (0.24), residues: 421 sheet: -1.65 (0.27), residues: 288 loop : -0.98 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 213 HIS 0.009 0.002 HIS A 100 PHE 0.027 0.003 PHE A 172 TYR 0.029 0.003 TYR A 258 ARG 0.005 0.001 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 126 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 282 ASP cc_start: 0.7004 (t70) cc_final: 0.6567 (t0) REVERT: D 71 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8249 (tm-30) REVERT: B 208 GLU cc_start: 0.8153 (tt0) cc_final: 0.7827 (tt0) REVERT: C 211 TRP cc_start: 0.6825 (OUTLIER) cc_final: 0.5895 (m-10) REVERT: G 42 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7393 (mm-30) REVERT: H 50 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7203 (t80) REVERT: H 55 SER cc_start: 0.7870 (m) cc_final: 0.7413 (p) outliers start: 40 outliers final: 23 residues processed: 158 average time/residue: 0.1983 time to fit residues: 44.0246 Evaluate side-chains 147 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.0370 chunk 71 optimal weight: 0.5980 chunk 106 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8826 Z= 0.214 Angle : 0.625 8.850 12040 Z= 0.324 Chirality : 0.043 0.161 1431 Planarity : 0.004 0.053 1536 Dihedral : 5.562 68.169 1275 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.91 % Allowed : 17.72 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1183 helix: 0.78 (0.25), residues: 422 sheet: -1.51 (0.28), residues: 284 loop : -0.78 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 82 HIS 0.006 0.001 HIS C 91 PHE 0.015 0.001 PHE A 93 TYR 0.017 0.002 TYR C 105 ARG 0.008 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 128 time to evaluate : 0.964 Fit side-chains REVERT: A 94 THR cc_start: 0.6861 (p) cc_final: 0.6579 (p) REVERT: A 282 ASP cc_start: 0.6967 (t70) cc_final: 0.6694 (t0) REVERT: D 70 MET cc_start: 0.7774 (mmm) cc_final: 0.7562 (mmt) REVERT: D 74 ARG cc_start: 0.5131 (OUTLIER) cc_final: 0.4360 (mtt90) REVERT: B 309 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7275 (mt-10) REVERT: G 42 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7351 (mm-30) REVERT: H 55 SER cc_start: 0.7857 (m) cc_final: 0.7387 (p) outliers start: 24 outliers final: 17 residues processed: 146 average time/residue: 0.2032 time to fit residues: 41.0959 Evaluate side-chains 136 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8826 Z= 0.231 Angle : 0.619 8.729 12040 Z= 0.320 Chirality : 0.042 0.142 1431 Planarity : 0.005 0.053 1536 Dihedral : 5.353 63.958 1275 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.61 % Allowed : 16.99 % Favored : 78.40 % 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: -0.55 (0.25), residues: 1183 helix: 0.94 (0.25), residues: 423 sheet: -1.41 (0.29), residues: 287 loop : -0.73 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 82 HIS 0.005 0.001 HIS C 91 PHE 0.020 0.002 PHE H 212 TYR 0.016 0.002 TYR A 258 ARG 0.005 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 0.981 Fit side-chains REVERT: A 94 THR cc_start: 0.6710 (p) cc_final: 0.6471 (p) REVERT: A 282 ASP cc_start: 0.7020 (t70) cc_final: 0.6750 (t0) REVERT: D 74 ARG cc_start: 0.4897 (OUTLIER) cc_final: 0.4270 (mtt90) REVERT: B 191 THR cc_start: 0.7504 (p) cc_final: 0.7227 (p) REVERT: B 309 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7328 (mt-10) REVERT: C 211 TRP cc_start: 0.6591 (OUTLIER) cc_final: 0.5742 (m-10) REVERT: G 42 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7381 (mm-30) REVERT: H 55 SER cc_start: 0.7884 (m) cc_final: 0.7419 (p) outliers start: 38 outliers final: 27 residues processed: 151 average time/residue: 0.2025 time to fit residues: 42.8952 Evaluate side-chains 151 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 27 optimal weight: 0.0980 chunk 113 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8826 Z= 0.225 Angle : 0.616 8.571 12040 Z= 0.317 Chirality : 0.042 0.148 1431 Planarity : 0.004 0.054 1536 Dihedral : 5.253 65.021 1275 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.00 % Allowed : 19.17 % Favored : 76.82 % 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: -0.48 (0.25), residues: 1183 helix: 1.03 (0.25), residues: 423 sheet: -1.39 (0.29), residues: 287 loop : -0.71 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.003 0.001 HIS C 183 PHE 0.025 0.002 PHE H 212 TYR 0.016 0.002 TYR A 258 ARG 0.004 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 118 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 94 THR cc_start: 0.6668 (p) cc_final: 0.6434 (p) REVERT: A 282 ASP cc_start: 0.7001 (t70) cc_final: 0.6738 (t0) REVERT: D 74 ARG cc_start: 0.4988 (OUTLIER) cc_final: 0.4241 (mtt90) REVERT: B 191 THR cc_start: 0.7316 (p) cc_final: 0.7056 (p) REVERT: B 309 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7330 (mt-10) REVERT: G 42 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7352 (mm-30) outliers start: 33 outliers final: 28 residues processed: 144 average time/residue: 0.2240 time to fit residues: 46.5579 Evaluate side-chains 145 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 175 TYR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 0.0270 chunk 63 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8826 Z= 0.235 Angle : 0.620 8.500 12040 Z= 0.319 Chirality : 0.042 0.149 1431 Planarity : 0.004 0.054 1536 Dihedral : 5.183 60.329 1275 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 5.10 % Allowed : 19.17 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.25), residues: 1183 helix: 1.04 (0.25), residues: 422 sheet: -1.42 (0.29), residues: 287 loop : -0.78 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.004 0.001 HIS C 91 PHE 0.018 0.002 PHE H 212 TYR 0.016 0.002 TYR A 258 ARG 0.004 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 120 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.6314 (m110) cc_final: 0.6049 (m-40) REVERT: A 94 THR cc_start: 0.6750 (p) cc_final: 0.6533 (p) REVERT: A 282 ASP cc_start: 0.7005 (t70) cc_final: 0.6741 (t0) REVERT: D 74 ARG cc_start: 0.5011 (OUTLIER) cc_final: 0.4263 (mtt90) REVERT: B 191 THR cc_start: 0.7482 (p) cc_final: 0.7225 (p) REVERT: B 309 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7317 (mt-10) REVERT: C 211 TRP cc_start: 0.6575 (OUTLIER) cc_final: 0.5750 (m-10) REVERT: G 42 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7349 (mm-30) outliers start: 42 outliers final: 36 residues processed: 150 average time/residue: 0.1930 time to fit residues: 41.0710 Evaluate side-chains 157 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 119 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8826 Z= 0.282 Angle : 0.649 8.418 12040 Z= 0.333 Chirality : 0.043 0.151 1431 Planarity : 0.005 0.058 1536 Dihedral : 5.294 62.992 1275 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.70 % Allowed : 19.30 % Favored : 75.00 % 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: -0.60 (0.25), residues: 1183 helix: 0.99 (0.25), residues: 421 sheet: -1.50 (0.29), residues: 289 loop : -0.80 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 82 HIS 0.004 0.001 HIS C 91 PHE 0.025 0.002 PHE H 212 TYR 0.018 0.002 TYR A 258 ARG 0.004 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 116 time to evaluate : 0.951 Fit side-chains REVERT: A 94 THR cc_start: 0.6703 (p) cc_final: 0.6484 (p) REVERT: A 282 ASP cc_start: 0.7008 (t70) cc_final: 0.6742 (t0) REVERT: D 74 ARG cc_start: 0.5137 (OUTLIER) cc_final: 0.4293 (mtt90) REVERT: B 191 THR cc_start: 0.7637 (p) cc_final: 0.7391 (p) REVERT: C 211 TRP cc_start: 0.6590 (OUTLIER) cc_final: 0.5765 (m-10) REVERT: G 42 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7351 (mm-30) REVERT: H 50 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.6533 (t80) outliers start: 47 outliers final: 36 residues processed: 153 average time/residue: 0.2074 time to fit residues: 45.1481 Evaluate side-chains 153 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 114 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 94 optimal weight: 0.0980 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN B 245 HIS ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8826 Z= 0.236 Angle : 0.634 9.629 12040 Z= 0.324 Chirality : 0.042 0.153 1431 Planarity : 0.004 0.054 1536 Dihedral : 5.162 63.301 1275 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 5.58 % Allowed : 20.15 % Favored : 74.27 % 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: -0.53 (0.25), residues: 1183 helix: 1.04 (0.25), residues: 423 sheet: -1.42 (0.29), residues: 281 loop : -0.81 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.021 0.002 PHE H 212 TYR 0.016 0.002 TYR A 258 ARG 0.004 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 116 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 94 THR cc_start: 0.6730 (p) cc_final: 0.6504 (p) REVERT: A 282 ASP cc_start: 0.6970 (t70) cc_final: 0.6725 (t0) REVERT: D 71 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: D 74 ARG cc_start: 0.4996 (OUTLIER) cc_final: 0.4248 (mtt90) REVERT: B 191 THR cc_start: 0.7532 (p) cc_final: 0.7288 (p) REVERT: B 309 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7194 (mt-10) REVERT: C 211 TRP cc_start: 0.6534 (OUTLIER) cc_final: 0.5722 (m-10) REVERT: G 42 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7330 (mm-30) REVERT: H 50 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.6415 (t80) outliers start: 46 outliers final: 40 residues processed: 150 average time/residue: 0.1992 time to fit residues: 42.0185 Evaluate side-chains 157 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 113 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.5980 chunk 67 optimal weight: 0.0980 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 116 optimal weight: 0.1980 chunk 107 optimal weight: 0.0020 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8826 Z= 0.194 Angle : 0.617 11.140 12040 Z= 0.313 Chirality : 0.041 0.156 1431 Planarity : 0.004 0.055 1536 Dihedral : 5.028 63.058 1275 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.98 % Allowed : 20.39 % Favored : 74.64 % 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: -0.36 (0.25), residues: 1183 helix: 1.15 (0.26), residues: 422 sheet: -1.25 (0.30), residues: 267 loop : -0.77 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS C 183 PHE 0.021 0.001 PHE H 212 TYR 0.013 0.001 TYR A 258 ARG 0.004 0.000 ARG C 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 115 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 282 ASP cc_start: 0.6907 (t70) cc_final: 0.6691 (t0) REVERT: D 74 ARG cc_start: 0.5088 (OUTLIER) cc_final: 0.4269 (mtt90) REVERT: B 191 THR cc_start: 0.7438 (p) cc_final: 0.7180 (p) REVERT: B 309 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7165 (mt-10) REVERT: G 42 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7264 (mm-30) outliers start: 41 outliers final: 35 residues processed: 146 average time/residue: 0.2000 time to fit residues: 41.2464 Evaluate side-chains 148 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 159 CYS Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 194 ASN Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 95 optimal weight: 0.0770 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 81 optimal weight: 0.0980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.138975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.117899 restraints weight = 17308.269| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.51 r_work: 0.3738 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8826 Z= 0.214 Angle : 0.626 9.456 12040 Z= 0.317 Chirality : 0.042 0.163 1431 Planarity : 0.004 0.054 1536 Dihedral : 5.010 62.761 1275 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.73 % Allowed : 20.63 % Favored : 74.64 % 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: -0.43 (0.25), residues: 1183 helix: 1.16 (0.26), residues: 422 sheet: -1.38 (0.29), residues: 281 loop : -0.78 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS C 183 PHE 0.021 0.001 PHE H 212 TYR 0.015 0.001 TYR A 258 ARG 0.004 0.000 ARG C 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2216.66 seconds wall clock time: 40 minutes 53.41 seconds (2453.41 seconds total)