Starting phenix.real_space_refine on Fri Nov 15 08:58:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia2_35292/11_2024/8ia2_35292.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia2_35292/11_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_35292/11_2024/8ia2_35292.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia2_35292/11_2024/8ia2_35292.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia2_35292/11_2024/8ia2_35292.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia2_35292/11_2024/8ia2_35292.cif" } 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. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 5.82, per 1000 atoms: 0.67 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.1 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: 1.09 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: 2.50 Time building geometry restraints manager: 2.65 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: 0.00 - 1.54: 11425 1.54 - 3.08: 490 3.08 - 4.62: 106 4.62 - 6.16: 16 6.16 - 7.70: 3 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 3.120 nonbonded pdb=" O GLN B 333 " pdb=" NE2 GLN B 333 " model vdw 2.202 3.120 nonbonded pdb=" N GLN D 3 " pdb=" OE1 GLN D 3 " model vdw 2.207 3.120 nonbonded pdb=" O VAL A 58 " pdb=" OG1 THR A 62 " model vdw 2.211 3.040 nonbonded pdb=" O SER A 237 " pdb=" OG1 THR A 238 " model vdw 2.213 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.280 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.020 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.947 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: 0.2309 time to fit residues: 45.1660 Evaluate side-chains 128 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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: 0.7980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 106 optimal weight: 0.0670 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1455 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 : 0.684 8.734 12040 Z= 0.358 Chirality : 0.045 0.155 1431 Planarity : 0.005 0.051 1536 Dihedral : 6.221 64.276 1279 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.94 % Allowed : 11.77 % Favored : 86.29 % 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: -0.67 (0.24), residues: 1183 helix: 0.53 (0.25), residues: 421 sheet: -1.05 (0.29), residues: 277 loop : -0.79 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 82 HIS 0.007 0.001 HIS A 100 PHE 0.021 0.002 PHE H 212 TYR 0.019 0.002 TYR A 181 ARG 0.003 0.001 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 146 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.948 Fit side-chains REVERT: A 282 ASP cc_start: 0.6877 (t70) cc_final: 0.6386 (t0) REVERT: A 290 TYR cc_start: 0.8258 (m-80) cc_final: 0.7879 (m-80) REVERT: C 234 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8692 (m-80) REVERT: G 42 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7311 (mm-30) REVERT: H 50 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.6742 (t80) REVERT: H 55 SER cc_start: 0.7833 (m) cc_final: 0.7446 (p) REVERT: H 220 GLU cc_start: 0.7051 (mp0) cc_final: 0.6727 (mm-30) outliers start: 16 outliers final: 11 residues processed: 141 average time/residue: 0.2124 time to fit residues: 41.1263 Evaluate side-chains 134 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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: 5.9990 chunk 32 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8826 Z= 0.224 Angle : 0.625 8.444 12040 Z= 0.326 Chirality : 0.043 0.152 1431 Planarity : 0.004 0.058 1536 Dihedral : 5.817 67.383 1278 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.40 % Allowed : 13.47 % Favored : 83.13 % 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: -0.47 (0.25), residues: 1183 helix: 0.83 (0.25), residues: 421 sheet: -1.14 (0.28), residues: 288 loop : -0.66 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 82 HIS 0.006 0.001 HIS A 100 PHE 0.014 0.002 PHE A 93 TYR 0.014 0.002 TYR A 181 ARG 0.004 0.000 ARG C 304 *********************** 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 154 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 94 THR cc_start: 0.6849 (p) cc_final: 0.6603 (p) REVERT: A 282 ASP cc_start: 0.7050 (t70) cc_final: 0.6786 (t0) REVERT: A 290 TYR cc_start: 0.8297 (m-80) cc_final: 0.7965 (m-80) REVERT: D 74 ARG cc_start: 0.4910 (OUTLIER) cc_final: 0.4313 (mtt90) REVERT: C 304 ARG cc_start: 0.5423 (mmp-170) cc_final: 0.4566 (mmp-170) REVERT: G 42 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7329 (mm-30) REVERT: H 55 SER cc_start: 0.7865 (m) cc_final: 0.7406 (p) outliers start: 28 outliers final: 18 residues processed: 145 average time/residue: 0.2385 time to fit residues: 47.7639 Evaluate side-chains 139 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE 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 217 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 232 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 210 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 50 optimal weight: 0.0470 chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 0.0970 chunk 30 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 330 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8826 Z= 0.196 Angle : 0.601 8.476 12040 Z= 0.311 Chirality : 0.043 0.154 1431 Planarity : 0.004 0.060 1536 Dihedral : 5.539 65.114 1278 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.91 % Allowed : 15.41 % Favored : 81.67 % 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: -0.30 (0.25), residues: 1183 helix: 1.03 (0.25), residues: 422 sheet: -1.09 (0.28), residues: 289 loop : -0.59 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.006 0.001 HIS C 91 PHE 0.026 0.001 PHE H 212 TYR 0.012 0.001 TYR A 258 ARG 0.004 0.000 ARG C 304 *********************** 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 148 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 94 THR cc_start: 0.6768 (p) cc_final: 0.6510 (p) REVERT: A 282 ASP cc_start: 0.7034 (t70) cc_final: 0.6757 (t0) REVERT: A 290 TYR cc_start: 0.8348 (m-80) cc_final: 0.8081 (m-80) REVERT: D 74 ARG cc_start: 0.4922 (OUTLIER) cc_final: 0.4332 (mtt90) REVERT: B 309 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7234 (mt-10) REVERT: G 42 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7269 (mm-30) REVERT: H 55 SER cc_start: 0.7875 (m) cc_final: 0.7405 (p) outliers start: 24 outliers final: 20 residues processed: 139 average time/residue: 0.1963 time to fit residues: 38.2950 Evaluate side-chains 141 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ILE 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 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 348 LEU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 116 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS H 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8826 Z= 0.338 Angle : 0.676 8.341 12040 Z= 0.351 Chirality : 0.045 0.146 1431 Planarity : 0.005 0.059 1536 Dihedral : 5.718 65.859 1278 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.22 % Allowed : 14.68 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1183 helix: 0.82 (0.25), residues: 422 sheet: -1.32 (0.28), residues: 288 loop : -0.63 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.006 0.001 HIS C 91 PHE 0.028 0.002 PHE H 212 TYR 0.021 0.002 TYR A 258 ARG 0.004 0.000 ARG C 304 *********************** 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 164 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 THR cc_start: 0.6897 (p) cc_final: 0.6636 (p) REVERT: A 290 TYR cc_start: 0.8332 (m-80) cc_final: 0.7994 (m-80) REVERT: D 74 ARG cc_start: 0.5191 (OUTLIER) cc_final: 0.4315 (mtt90) REVERT: C 211 TRP cc_start: 0.6679 (OUTLIER) cc_final: 0.5813 (m-10) REVERT: G 42 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7309 (mm-30) REVERT: H 50 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.6871 (t80) REVERT: H 55 SER cc_start: 0.7894 (OUTLIER) cc_final: 0.7434 (p) outliers start: 43 outliers final: 31 residues processed: 153 average time/residue: 0.1972 time to fit residues: 42.9449 Evaluate side-chains 152 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 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 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 296 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 211 TRP Chi-restraints excluded: chain C residue 263 THR 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 55 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 116 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 0.0040 chunk 109 optimal weight: 0.0870 overall best weight: 0.3570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 HIS B 330 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2579 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= 0.189 Angle : 0.597 8.109 12040 Z= 0.309 Chirality : 0.042 0.145 1431 Planarity : 0.004 0.061 1536 Dihedral : 5.190 66.570 1275 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.40 % Allowed : 17.84 % Favored : 78.76 % 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: -0.30 (0.25), residues: 1183 helix: 1.11 (0.25), residues: 420 sheet: -1.16 (0.29), residues: 277 loop : -0.64 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS A 100 PHE 0.012 0.001 PHE A 93 TYR 0.014 0.001 TYR A 258 ARG 0.005 0.000 ARG D 74 *********************** 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 to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 THR cc_start: 0.6787 (p) cc_final: 0.6523 (p) REVERT: A 290 TYR cc_start: 0.8349 (m-80) cc_final: 0.8019 (m-80) REVERT: D 74 ARG cc_start: 0.4772 (OUTLIER) cc_final: 0.4335 (mtt90) REVERT: B 309 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7060 (mt-10) REVERT: G 42 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7302 (mm-30) REVERT: H 55 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7392 (p) outliers start: 28 outliers final: 22 residues processed: 140 average time/residue: 0.2160 time to fit residues: 42.1766 Evaluate side-chains 138 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 205 VAL Chi-restraints excluded: chain A residue 265 MET 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 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 263 THR 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 H residue 55 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 116 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 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: 0.9980 chunk 82 optimal weight: 0.0470 chunk 95 optimal weight: 9.9990 chunk 63 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 68 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 69 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 overall best weight: 0.2856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2844 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= 0.174 Angle : 0.590 8.091 12040 Z= 0.302 Chirality : 0.041 0.146 1431 Planarity : 0.004 0.060 1536 Dihedral : 4.987 66.845 1275 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.40 % Allowed : 18.08 % Favored : 78.52 % 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: -0.11 (0.25), residues: 1183 helix: 1.22 (0.26), residues: 421 sheet: -0.89 (0.31), residues: 261 loop : -0.62 (0.30), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE H 212 TYR 0.012 0.001 TYR A 258 ARG 0.005 0.000 ARG D 74 *********************** 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 150 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 TYR cc_start: 0.8326 (m-80) cc_final: 0.8016 (m-80) REVERT: D 28 VAL cc_start: 0.6587 (m) cc_final: 0.6330 (m) REVERT: D 70 MET cc_start: 0.8045 (mmm) cc_final: 0.7752 (mmt) REVERT: D 74 ARG cc_start: 0.4700 (OUTLIER) cc_final: 0.4272 (mtt90) REVERT: B 309 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7053 (mt-10) REVERT: C 304 ARG cc_start: 0.5329 (mmp-170) cc_final: 0.5077 (mmp-170) REVERT: G 42 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7238 (mm-30) REVERT: H 6 GLU cc_start: 0.4368 (mp0) cc_final: 0.4011 (mp0) REVERT: H 55 SER cc_start: 0.8053 (OUTLIER) cc_final: 0.7574 (p) outliers start: 28 outliers final: 23 residues processed: 141 average time/residue: 0.2041 time to fit residues: 40.4045 Evaluate side-chains 138 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 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 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 105 TYR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 284 LEU 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 97 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 172 THR 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: 0.0270 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 71 optimal weight: 0.7980 chunk 76 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2887 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 : 0.599 8.064 12040 Z= 0.306 Chirality : 0.042 0.148 1431 Planarity : 0.004 0.060 1536 Dihedral : 4.977 65.314 1275 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.88 % Allowed : 18.08 % Favored : 78.03 % 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: -0.12 (0.25), residues: 1183 helix: 1.28 (0.26), residues: 416 sheet: -1.00 (0.30), residues: 276 loop : -0.60 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.003 0.001 HIS H 35 PHE 0.033 0.001 PHE H 212 TYR 0.015 0.001 TYR A 258 ARG 0.005 0.000 ARG C 137 *********************** 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 148 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 TYR cc_start: 0.8313 (m-80) cc_final: 0.8011 (m-80) REVERT: D 28 VAL cc_start: 0.6491 (m) cc_final: 0.6082 (m) REVERT: D 74 ARG cc_start: 0.4746 (OUTLIER) cc_final: 0.4276 (mtt90) REVERT: B 309 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7023 (mt-10) REVERT: G 42 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7235 (mm-30) REVERT: H 55 SER cc_start: 0.8066 (OUTLIER) cc_final: 0.7625 (p) outliers start: 32 outliers final: 29 residues processed: 140 average time/residue: 0.1975 time to fit residues: 38.7700 Evaluate side-chains 146 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 301 VAL Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 296 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 105 TYR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 266 HIS 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 55 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 116 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 32 optimal weight: 0.0980 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.0970 chunk 104 optimal weight: 0.3980 chunk 69 optimal weight: 4.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8826 Z= 0.210 Angle : 0.611 9.925 12040 Z= 0.311 Chirality : 0.042 0.150 1431 Planarity : 0.004 0.062 1536 Dihedral : 5.017 66.331 1275 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.73 % Allowed : 17.23 % Favored : 78.03 % 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: -0.10 (0.25), residues: 1183 helix: 1.28 (0.26), residues: 415 sheet: -0.99 (0.30), residues: 276 loop : -0.56 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS A 100 PHE 0.025 0.001 PHE H 212 TYR 0.016 0.001 TYR A 258 ARG 0.005 0.000 ARG D 74 *********************** 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 155 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 TYR cc_start: 0.8279 (m-80) cc_final: 0.7974 (m-80) REVERT: D 28 VAL cc_start: 0.6445 (m) cc_final: 0.6080 (m) REVERT: D 71 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: D 74 ARG cc_start: 0.4819 (OUTLIER) cc_final: 0.4244 (mtt90) REVERT: B 309 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7016 (mt-10) REVERT: H 55 SER cc_start: 0.8102 (OUTLIER) cc_final: 0.7668 (p) outliers start: 39 outliers final: 31 residues processed: 146 average time/residue: 0.1959 time to fit residues: 40.2811 Evaluate side-chains 145 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 295 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 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 105 TYR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 263 THR 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 H residue 30 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 116 THR 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 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 77 optimal weight: 0.0970 chunk 116 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 9 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8826 Z= 0.219 Angle : 0.626 10.398 12040 Z= 0.318 Chirality : 0.042 0.156 1431 Planarity : 0.004 0.061 1536 Dihedral : 5.036 67.135 1275 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.13 % Allowed : 18.08 % Favored : 77.79 % 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: -0.14 (0.25), residues: 1183 helix: 1.25 (0.26), residues: 413 sheet: -1.04 (0.30), residues: 269 loop : -0.57 (0.30), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.028 0.001 PHE H 212 TYR 0.016 0.002 TYR A 258 ARG 0.006 0.000 ARG C 137 ********************** 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 147 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 TYR cc_start: 0.8274 (m-80) cc_final: 0.7968 (m-80) REVERT: D 28 VAL cc_start: 0.6371 (m) cc_final: 0.5998 (m) REVERT: D 71 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: D 74 ARG cc_start: 0.4849 (OUTLIER) cc_final: 0.4218 (mtt90) REVERT: B 309 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7028 (mt-10) REVERT: H 55 SER cc_start: 0.8035 (OUTLIER) cc_final: 0.7594 (p) outliers start: 34 outliers final: 31 residues processed: 139 average time/residue: 0.1993 time to fit residues: 38.9056 Evaluate side-chains 145 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 295 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 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 105 TYR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 263 THR 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 H residue 30 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 116 THR 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 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.0770 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 95 optimal weight: 0.1980 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.137517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.116790 restraints weight = 17404.865| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.46 r_work: 0.3762 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8826 Z= 0.214 Angle : 0.617 9.042 12040 Z= 0.315 Chirality : 0.042 0.155 1431 Planarity : 0.004 0.061 1536 Dihedral : 5.033 67.771 1275 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.13 % Allowed : 18.33 % Favored : 77.55 % 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: -0.15 (0.25), residues: 1183 helix: 1.23 (0.26), residues: 413 sheet: -1.03 (0.30), residues: 269 loop : -0.57 (0.30), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.028 0.001 PHE H 212 TYR 0.016 0.002 TYR A 258 ARG 0.006 0.000 ARG C 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2152.85 seconds wall clock time: 40 minutes 15.89 seconds (2415.89 seconds total)