Starting phenix.real_space_refine on Sat Dec 9 01:48:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx0_24721/12_2023/7rx0_24721_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx0_24721/12_2023/7rx0_24721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx0_24721/12_2023/7rx0_24721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx0_24721/12_2023/7rx0_24721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx0_24721/12_2023/7rx0_24721_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rx0_24721/12_2023/7rx0_24721_updated.pdb" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.010 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 55 5.16 5 C 6047 2.51 5 N 1679 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 152": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 327": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9673 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2482 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "G" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 395 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'TRANS': 78} Chain breaks: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'UNK:plan-1': 79} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3349 Classifications: {'peptide': 428} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N VAL C 47 " occ=0.71 ... (5 atoms not shown) pdb=" CG2 VAL C 47 " occ=0.71 residue: pdb=" N PHE C 86 " occ=0.51 ... (9 atoms not shown) pdb=" CZ PHE C 86 " occ=0.51 residue: pdb=" N PHE C 91 " occ=0.63 ... (9 atoms not shown) pdb=" CZ PHE C 91 " occ=0.63 residue: pdb=" N LEU C 168 " occ=0.62 ... (6 atoms not shown) pdb=" CD2 LEU C 168 " occ=0.62 residue: pdb=" N SER C 304 " occ=0.51 ... (4 atoms not shown) pdb=" OG SER C 304 " occ=0.51 Time building chain proxies: 5.73, per 1000 atoms: 0.59 Number of scatterers: 9673 At special positions: 0 Unit cell: (81.9, 111.8, 118.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 55 16.00 P 9 15.00 Mg 1 11.99 O 1882 8.00 N 1679 7.00 C 6047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.38 Conformation dependent library (CDL) restraints added in 1.7 seconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 9 sheets defined 46.1% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'C' and resid 27 through 32 removed outlier: 4.841A pdb=" N HIS C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 removed outlier: 4.949A pdb=" N GLN C 76 " --> pdb=" O GLN C 72 " (cutoff:3.500A) Proline residue: C 77 - end of helix removed outlier: 4.830A pdb=" N PHE C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 103 No H-bonds generated for 'chain 'C' and resid 100 through 103' Processing helix chain 'C' and resid 119 through 131 Processing helix chain 'C' and resid 189 through 202 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 267 through 288 removed outlier: 3.934A pdb=" N GLN C 274 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 313 removed outlier: 4.367A pdb=" N ASP C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N SER C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 346 removed outlier: 3.549A pdb=" N ARG C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 346 " --> pdb=" O TYR C 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 25 Processing helix chain 'G' and resid 51 through 61 Processing helix chain 'G' and resid 81 through 91 Processing helix chain 'A' and resid 11 through 27 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 86 removed outlier: 4.374A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.880A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.276A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 278 through 281 No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 288 through 296 removed outlier: 4.234A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 325 through 338 Processing helix chain 'A' and resid 382 through 401 Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 41 through 47 removed outlier: 3.742A pdb=" N GLU B 47 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 111 through 128 removed outlier: 3.855A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.625A pdb=" N GLY B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 Proline residue: B 184 - end of helix removed outlier: 4.178A pdb=" N VAL B 195 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN B 197 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 224 through 240 removed outlier: 4.002A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 382 through 401 removed outlier: 4.656A pdb=" N GLU B 393 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE B 399 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG B 400 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.958A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 436 Processing sheet with id= A, first strand: chain 'C' and resid 20 through 22 removed outlier: 7.409A pdb=" N ARG C 21 " --> pdb=" O MET C 322 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ALA C 324 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE C 91 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 323 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N CYS C 325 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS C 249 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 90 " --> pdb=" O HIS C 249 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 251 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER C 246 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 225 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 38 through 41 Processing sheet with id= C, first strand: chain 'C' and resid 167 through 170 Processing sheet with id= D, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.203A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 5 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N PHE A 135 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE A 7 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 9 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N HIS A 139 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= F, first strand: chain 'A' and resid 269 through 273 Processing sheet with id= G, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.194A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N VAL B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ALA B 9 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N HIS B 139 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU B 137 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ASN B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N HIS B 139 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 53 through 56 Processing sheet with id= I, first strand: chain 'B' and resid 269 through 273 403 hydrogen bonds defined for protein. 1059 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: 2.62 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3265 1.34 - 1.46: 2174 1.46 - 1.58: 4324 1.58 - 1.70: 13 1.70 - 1.81: 89 Bond restraints: 9865 Sorted by residual: bond pdb=" O3B G2P B 501 " pdb=" PG G2P B 501 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" O1A G2P B 501 " pdb=" PA G2P B 501 " ideal model delta sigma weight residual 1.507 1.611 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" O1B G2P B 501 " pdb=" PB G2P B 501 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C5 GTP A 501 " pdb=" C6 GTP A 501 " ideal model delta sigma weight residual 1.390 1.481 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O3A ANP C1401 " pdb=" PB ANP C1401 " ideal model delta sigma weight residual 1.700 1.610 0.090 2.00e-02 2.50e+03 2.03e+01 ... (remaining 9860 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.79: 300 106.79 - 114.14: 5755 114.14 - 121.48: 5071 121.48 - 128.82: 2219 128.82 - 136.17: 62 Bond angle restraints: 13407 Sorted by residual: angle pdb=" C THR C 205 " pdb=" CA THR C 205 " pdb=" CB THR C 205 " ideal model delta sigma weight residual 110.42 124.13 -13.71 1.99e+00 2.53e-01 4.75e+01 angle pdb=" C HIS C 204 " pdb=" N THR C 205 " pdb=" CA THR C 205 " ideal model delta sigma weight residual 121.54 111.50 10.04 1.91e+00 2.74e-01 2.76e+01 angle pdb=" N SER C 215 " pdb=" CA SER C 215 " pdb=" C SER C 215 " ideal model delta sigma weight residual 110.91 115.77 -4.86 1.17e+00 7.31e-01 1.73e+01 angle pdb=" PA G2P B 501 " pdb=" C3A G2P B 501 " pdb=" PB G2P B 501 " ideal model delta sigma weight residual 120.83 109.51 11.32 3.00e+00 1.11e-01 1.42e+01 angle pdb=" N THR C 208 " pdb=" CA THR C 208 " pdb=" C THR C 208 " ideal model delta sigma weight residual 108.96 103.00 5.96 1.59e+00 3.96e-01 1.41e+01 ... (remaining 13402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.70: 5774 33.70 - 67.39: 119 67.39 - 101.08: 13 101.08 - 134.78: 2 134.78 - 168.47: 4 Dihedral angle restraints: 5912 sinusoidal: 2282 harmonic: 3630 Sorted by residual: dihedral pdb=" C THR C 205 " pdb=" N THR C 205 " pdb=" CA THR C 205 " pdb=" CB THR C 205 " ideal model delta harmonic sigma weight residual -122.00 -147.69 25.69 0 2.50e+00 1.60e-01 1.06e+02 dihedral pdb=" N THR C 205 " pdb=" C THR C 205 " pdb=" CA THR C 205 " pdb=" CB THR C 205 " ideal model delta harmonic sigma weight residual 123.40 142.70 -19.30 0 2.50e+00 1.60e-01 5.96e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.26 -168.47 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 5909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 1503 0.199 - 0.398: 1 0.398 - 0.597: 0 0.597 - 0.796: 0 0.796 - 0.995: 1 Chirality restraints: 1505 Sorted by residual: chirality pdb=" CA THR C 205 " pdb=" N THR C 205 " pdb=" C THR C 205 " pdb=" CB THR C 205 " both_signs ideal model delta sigma weight residual False 2.53 1.53 0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CA HIS C 204 " pdb=" N HIS C 204 " pdb=" C HIS C 204 " pdb=" CB HIS C 204 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C3' ANP C1401 " pdb=" C2' ANP C1401 " pdb=" C4' ANP C1401 " pdb=" O3' ANP C1401 " both_signs ideal model delta sigma weight residual False -2.36 -2.54 0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 1502 not shown) Planarity restraints: 1749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 202 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C ALA C 202 " 0.031 2.00e-02 2.50e+03 pdb=" O ALA C 202 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG C 203 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET B 269 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO B 270 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 31 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 32 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.021 5.00e-02 4.00e+02 ... (remaining 1746 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 64 2.31 - 2.96: 5398 2.96 - 3.61: 15704 3.61 - 4.25: 22971 4.25 - 4.90: 36351 Nonbonded interactions: 80488 Sorted by model distance: nonbonded pdb=" O ARG C 203 " pdb=" O GLY C 206 " model vdw 1.666 3.040 nonbonded pdb=" O2A G2P B 501 " pdb="MG MG B 502 " model vdw 1.777 2.170 nonbonded pdb=" C GLY C 199 " pdb=" NH1 ARG C 203 " model vdw 1.818 3.350 nonbonded pdb=" O2G G2P B 501 " pdb="MG MG B 502 " model vdw 1.923 2.170 nonbonded pdb=" OH TYR C 145 " pdb=" NH2 ARG C 203 " model vdw 1.968 2.520 ... (remaining 80483 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=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.050 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: 0.980 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.910 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: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 : 0.006 0.105 9865 Z= 0.399 Angle : 0.854 13.713 13407 Z= 0.458 Chirality : 0.051 0.995 1505 Planarity : 0.004 0.045 1749 Dihedral : 15.605 168.471 3576 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 29.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.08 % 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: -2.61 (0.22), residues: 1172 helix: -1.24 (0.20), residues: 491 sheet: -1.23 (0.31), residues: 198 loop : -2.37 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 346 HIS 0.008 0.002 HIS C 298 PHE 0.016 0.002 PHE C 248 TYR 0.013 0.002 TYR B 432 ARG 0.006 0.000 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.2580 time to fit residues: 102.9218 Evaluate side-chains 201 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 31 optimal weight: 40.0000 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 96 optimal weight: 30.0000 chunk 37 optimal weight: 50.0000 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 31 GLN A 101 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 337 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9865 Z= 0.253 Angle : 0.716 9.398 13407 Z= 0.356 Chirality : 0.044 0.204 1505 Planarity : 0.005 0.070 1749 Dihedral : 11.167 155.410 1435 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.03 % Allowed : 19.19 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.45 (0.23), residues: 1172 helix: -0.22 (0.23), residues: 488 sheet: -1.03 (0.31), residues: 211 loop : -1.59 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 346 HIS 0.007 0.001 HIS C 204 PHE 0.017 0.002 PHE B 268 TYR 0.041 0.002 TYR C 71 ARG 0.012 0.001 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 230 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 241 average time/residue: 0.2427 time to fit residues: 80.8202 Evaluate side-chains 214 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 196 time to evaluate : 1.092 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0864 time to fit residues: 4.3698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 60.0000 chunk 92 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 111 optimal weight: 50.0000 chunk 120 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 110 optimal weight: 40.0000 chunk 38 optimal weight: 60.0000 chunk 89 optimal weight: 20.0000 overall best weight: 9.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN C 76 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN A 342 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9865 Z= 0.275 Angle : 0.712 11.165 13407 Z= 0.353 Chirality : 0.043 0.249 1505 Planarity : 0.005 0.043 1749 Dihedral : 10.812 162.922 1435 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.43 % Allowed : 20.81 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.08 (0.24), residues: 1172 helix: 0.14 (0.23), residues: 482 sheet: -0.87 (0.32), residues: 205 loop : -1.42 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 346 HIS 0.005 0.001 HIS A 8 PHE 0.022 0.002 PHE C 153 TYR 0.026 0.002 TYR A 272 ARG 0.006 0.001 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 210 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 13 residues processed: 228 average time/residue: 0.2149 time to fit residues: 68.7321 Evaluate side-chains 201 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0974 time to fit residues: 3.7434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 40.0000 chunk 84 optimal weight: 40.0000 chunk 58 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 112 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 32 optimal weight: 50.0000 chunk 99 optimal weight: 40.0000 overall best weight: 10.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9865 Z= 0.286 Angle : 0.708 10.757 13407 Z= 0.353 Chirality : 0.043 0.188 1505 Planarity : 0.004 0.033 1749 Dihedral : 10.834 170.944 1435 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 24.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.13 % Allowed : 23.74 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -1.00 (0.24), residues: 1172 helix: 0.16 (0.23), residues: 482 sheet: -0.76 (0.33), residues: 203 loop : -1.38 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 346 HIS 0.005 0.001 HIS A 28 PHE 0.013 0.002 PHE C 153 TYR 0.031 0.002 TYR C 71 ARG 0.004 0.001 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 200 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 219 average time/residue: 0.2109 time to fit residues: 64.8247 Evaluate side-chains 202 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0931 time to fit residues: 4.3990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.8980 chunk 1 optimal weight: 30.0000 chunk 88 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 101 optimal weight: 40.0000 chunk 82 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 60 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9865 Z= 0.215 Angle : 0.691 12.111 13407 Z= 0.341 Chirality : 0.042 0.192 1505 Planarity : 0.004 0.048 1749 Dihedral : 10.690 169.842 1435 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.53 % Allowed : 24.95 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.84 (0.24), residues: 1172 helix: 0.19 (0.23), residues: 479 sheet: -0.51 (0.34), residues: 202 loop : -1.23 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 346 HIS 0.004 0.001 HIS C 298 PHE 0.014 0.001 PHE C 333 TYR 0.028 0.002 TYR A 272 ARG 0.005 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 233 average time/residue: 0.2147 time to fit residues: 70.0679 Evaluate side-chains 213 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 199 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0976 time to fit residues: 3.9757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 chunk 69 optimal weight: 30.0000 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 55 optimal weight: 50.0000 chunk 9 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9865 Z= 0.247 Angle : 0.729 13.576 13407 Z= 0.359 Chirality : 0.043 0.187 1505 Planarity : 0.005 0.043 1749 Dihedral : 10.768 172.494 1435 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.83 % Allowed : 27.07 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.80 (0.24), residues: 1172 helix: 0.19 (0.23), residues: 475 sheet: -0.42 (0.34), residues: 195 loop : -1.18 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 21 HIS 0.009 0.001 HIS B 107 PHE 0.033 0.002 PHE B 262 TYR 0.028 0.002 TYR A 272 ARG 0.006 0.001 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 218 average time/residue: 0.2176 time to fit residues: 67.2842 Evaluate side-chains 211 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 193 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0944 time to fit residues: 4.5326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 7.9990 chunk 67 optimal weight: 0.2980 chunk 86 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 118 optimal weight: 8.9990 chunk 74 optimal weight: 30.0000 chunk 72 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 73 optimal weight: 0.4980 chunk 47 optimal weight: 30.0000 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9865 Z= 0.209 Angle : 0.735 13.006 13407 Z= 0.361 Chirality : 0.043 0.174 1505 Planarity : 0.004 0.044 1749 Dihedral : 10.568 168.167 1435 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.31 % Allowed : 28.38 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.76 (0.24), residues: 1172 helix: 0.28 (0.23), residues: 467 sheet: -0.38 (0.34), residues: 195 loop : -1.23 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP B 346 HIS 0.005 0.001 HIS C 298 PHE 0.028 0.002 PHE B 262 TYR 0.024 0.002 TYR A 224 ARG 0.006 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 218 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 225 average time/residue: 0.2049 time to fit residues: 64.5626 Evaluate side-chains 203 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 198 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0853 time to fit residues: 2.1215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 30.0000 chunk 35 optimal weight: 50.0000 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 40.0000 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 11 optimal weight: 40.0000 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN A 380 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9865 Z= 0.247 Angle : 0.769 13.101 13407 Z= 0.378 Chirality : 0.043 0.178 1505 Planarity : 0.005 0.049 1749 Dihedral : 10.587 169.701 1435 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.52 % Allowed : 30.00 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.74 (0.24), residues: 1172 helix: 0.31 (0.23), residues: 474 sheet: -0.36 (0.34), residues: 191 loop : -1.25 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP B 346 HIS 0.007 0.001 HIS C 142 PHE 0.027 0.002 PHE B 262 TYR 0.031 0.002 TYR C 301 ARG 0.017 0.001 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 205 average time/residue: 0.2067 time to fit residues: 60.3958 Evaluate side-chains 208 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 198 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1022 time to fit residues: 3.1983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 33 optimal weight: 60.0000 chunk 99 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 116 optimal weight: 40.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9865 Z= 0.222 Angle : 0.768 12.566 13407 Z= 0.378 Chirality : 0.044 0.174 1505 Planarity : 0.005 0.040 1749 Dihedral : 10.512 167.427 1435 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.11 % Allowed : 30.30 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.72 (0.24), residues: 1172 helix: 0.32 (0.23), residues: 472 sheet: -0.24 (0.34), residues: 191 loop : -1.27 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 346 HIS 0.009 0.001 HIS C 142 PHE 0.024 0.002 PHE B 262 TYR 0.032 0.002 TYR A 272 ARG 0.015 0.001 ARG B 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 206 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 210 average time/residue: 0.2084 time to fit residues: 62.2895 Evaluate side-chains 200 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 190 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0962 time to fit residues: 3.2691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 40.0000 chunk 122 optimal weight: 7.9990 chunk 112 optimal weight: 40.0000 chunk 97 optimal weight: 20.0000 chunk 10 optimal weight: 40.0000 chunk 75 optimal weight: 30.0000 chunk 59 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 overall best weight: 5.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9865 Z= 0.224 Angle : 0.804 13.761 13407 Z= 0.388 Chirality : 0.046 0.441 1505 Planarity : 0.005 0.069 1749 Dihedral : 10.432 165.672 1435 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.30 % Allowed : 30.71 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1172 helix: 0.37 (0.24), residues: 469 sheet: -0.30 (0.34), residues: 190 loop : -1.21 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 346 HIS 0.006 0.001 HIS C 142 PHE 0.022 0.002 PHE B 262 TYR 0.030 0.002 TYR A 272 ARG 0.014 0.001 ARG B 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 203 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 204 average time/residue: 0.2154 time to fit residues: 61.9861 Evaluate side-chains 198 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0919 time to fit residues: 1.6885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.0570 chunk 89 optimal weight: 10.0000 chunk 14 optimal weight: 40.0000 chunk 27 optimal weight: 30.0000 chunk 97 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 12 optimal weight: 40.0000 chunk 18 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 overall best weight: 6.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN A 101 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.086073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.067367 restraints weight = 35255.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.069702 restraints weight = 18215.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.071254 restraints weight = 11398.365| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9865 Z= 0.232 Angle : 0.802 14.328 13407 Z= 0.391 Chirality : 0.044 0.166 1505 Planarity : 0.005 0.057 1749 Dihedral : 10.417 165.075 1435 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.11 % Allowed : 31.11 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1172 helix: 0.35 (0.24), residues: 475 sheet: -0.33 (0.34), residues: 190 loop : -1.18 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 346 HIS 0.009 0.001 HIS A 8 PHE 0.023 0.002 PHE B 262 TYR 0.030 0.002 TYR A 272 ARG 0.013 0.001 ARG B 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1961.58 seconds wall clock time: 36 minutes 54.26 seconds (2214.26 seconds total)