Starting phenix.real_space_refine on Thu Mar 14 08:11:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/03_2024/7rtb_24680_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/03_2024/7rtb_24680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/03_2024/7rtb_24680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/03_2024/7rtb_24680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/03_2024/7rtb_24680_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/03_2024/7rtb_24680_trim_updated.pdb" } resolution = 2.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 51 5.16 5 C 5693 2.51 5 N 1568 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "R GLU 139": "OE1" <-> "OE2" Residue "R GLU 292": "OE1" <-> "OE2" Residue "R GLU 294": "OE1" <-> "OE2" Residue "R GLU 408": "OE1" <-> "OE2" Residue "P GLU 21": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8972 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1949 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2796 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 14, 'TRANS': 369} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 419 Unresolved non-hydrogen angles: 553 Unresolved non-hydrogen dihedrals: 377 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 8, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 277 Chain: "P" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 236 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.46, per 1000 atoms: 0.61 Number of scatterers: 8972 At special positions: 0 Unit cell: (81.9, 96.85, 170.95, 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 51 16.00 O 1660 8.00 N 1568 7.00 C 5693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 2.0 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 11 sheets defined 39.3% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.733A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.657A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.970A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 33 through 55 Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 90 through 92 No H-bonds generated for 'chain 'R' and resid 90 through 92' Processing helix chain 'R' and resid 137 through 168 removed outlier: 3.612A pdb=" N ILE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 198 Processing helix chain 'R' and resid 200 through 210 removed outlier: 3.859A pdb=" N THR R 207 " --> pdb=" O TRP R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 214 through 222 Processing helix chain 'R' and resid 224 through 256 removed outlier: 4.145A pdb=" N VAL R 229 " --> pdb=" O CYS R 226 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE R 230 " --> pdb=" O ARG R 227 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU R 231 " --> pdb=" O LEU R 228 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU R 232 " --> pdb=" O VAL R 229 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL R 237 " --> pdb=" O GLN R 234 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU R 244 " --> pdb=" O TYR R 241 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU R 247 " --> pdb=" O LEU R 244 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA R 256 " --> pdb=" O THR R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 290 removed outlier: 3.695A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix removed outlier: 3.782A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.650A pdb=" N TYR R 289 " --> pdb=" O GLY R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 297 removed outlier: 3.796A pdb=" N TRP R 297 " --> pdb=" O GLU R 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 294 through 297' Processing helix chain 'R' and resid 310 through 337 removed outlier: 3.823A pdb=" N ASN R 320 " --> pdb=" O ALA R 316 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU R 322 " --> pdb=" O GLY R 318 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE R 324 " --> pdb=" O ASN R 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 360 removed outlier: 3.703A pdb=" N LEU R 354 " --> pdb=" O ALA R 350 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 370 Processing helix chain 'R' and resid 383 through 402 removed outlier: 5.104A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 422 removed outlier: 4.056A pdb=" N TRP R 420 " --> pdb=" O SER R 416 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 28 removed outlier: 5.113A pdb=" N LEU P 27 " --> pdb=" O VAL P 23 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA P 28 " --> pdb=" O ASN P 24 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.334A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.968A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.058A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.711A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.066A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.877A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.559A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.652A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.871A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 80 through 84 426 hydrogen bonds defined for protein. 1113 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: 2.73 Time building geometry restraints manager: 3.82 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: 2963 1.34 - 1.46: 2060 1.46 - 1.58: 4053 1.58 - 1.70: 0 1.70 - 1.81: 71 Bond restraints: 9147 Sorted by residual: bond pdb=" C ALA B 106 " pdb=" N PRO B 107 " ideal model delta sigma weight residual 1.333 1.379 -0.046 1.44e-02 4.82e+03 1.01e+01 bond pdb=" N ILE P 12 " pdb=" CA ILE P 12 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.82e+00 bond pdb=" N VAL P 23 " pdb=" CA VAL P 23 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.30e-02 5.92e+03 6.66e+00 bond pdb=" N ASN R 320 " pdb=" CA ASN R 320 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.36e+00 bond pdb=" N LEU P 26 " pdb=" CA LEU P 26 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.30e+00 ... (remaining 9142 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.37: 221 107.37 - 114.09: 5150 114.09 - 120.80: 4021 120.80 - 127.51: 2931 127.51 - 134.23: 83 Bond angle restraints: 12406 Sorted by residual: angle pdb=" C ALA B 106 " pdb=" N PRO B 107 " pdb=" CA PRO B 107 " ideal model delta sigma weight residual 119.47 125.13 -5.66 1.16e+00 7.43e-01 2.38e+01 angle pdb=" C GLY R 275 " pdb=" N VAL R 276 " pdb=" CA VAL R 276 " ideal model delta sigma weight residual 120.24 122.75 -2.51 6.30e-01 2.52e+00 1.59e+01 angle pdb=" N ASN P 24 " pdb=" CA ASN P 24 " pdb=" C ASN P 24 " ideal model delta sigma weight residual 111.28 107.62 3.66 1.09e+00 8.42e-01 1.13e+01 angle pdb=" N TRP R 417 " pdb=" CA TRP R 417 " pdb=" C TRP R 417 " ideal model delta sigma weight residual 113.55 109.58 3.97 1.26e+00 6.30e-01 9.92e+00 angle pdb=" C VAL R 276 " pdb=" CA VAL R 276 " pdb=" CB VAL R 276 " ideal model delta sigma weight residual 114.35 111.21 3.14 1.06e+00 8.90e-01 8.80e+00 ... (remaining 12401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4921 17.92 - 35.85: 388 35.85 - 53.77: 78 53.77 - 71.70: 17 71.70 - 89.62: 13 Dihedral angle restraints: 5417 sinusoidal: 2016 harmonic: 3401 Sorted by residual: dihedral pdb=" CA ASN R 320 " pdb=" C ASN R 320 " pdb=" N PHE R 321 " pdb=" CA PHE R 321 " ideal model delta harmonic sigma weight residual 180.00 157.67 22.33 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -120.51 34.51 1 1.00e+01 1.00e-02 1.69e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1084 0.045 - 0.090: 231 0.090 - 0.135: 73 0.135 - 0.180: 11 0.180 - 0.226: 2 Chirality restraints: 1401 Sorted by residual: chirality pdb=" CA LYS P 16 " pdb=" N LYS P 16 " pdb=" C LYS P 16 " pdb=" CB LYS P 16 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA LEU P 14 " pdb=" N LEU P 14 " pdb=" C LEU P 14 " pdb=" CB LEU P 14 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA LYS R 202 " pdb=" N LYS R 202 " pdb=" C LYS R 202 " pdb=" CB LYS R 202 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1398 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO N 88 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 315 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.33e+00 pdb=" C PHE R 315 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE R 315 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA R 316 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR P 13 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C TYR P 13 " 0.026 2.00e-02 2.50e+03 pdb=" O TYR P 13 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU P 14 " -0.009 2.00e-02 2.50e+03 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2347 2.80 - 3.33: 8462 3.33 - 3.85: 15244 3.85 - 4.38: 17770 4.38 - 4.90: 30179 Nonbonded interactions: 74002 Sorted by model distance: nonbonded pdb=" O LEU R 172 " pdb=" ND2 ASN R 177 " model vdw 2.277 2.520 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.311 2.440 nonbonded pdb=" NH2 ARG A 228 " pdb=" OE1 GLU A 230 " model vdw 2.335 2.520 nonbonded pdb=" NH2 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.339 2.520 nonbonded pdb=" OE1 GLN A 19 " pdb=" OG1 THR B 86 " model vdw 2.344 2.440 ... (remaining 73997 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=0.00 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: 1.320 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: 7.270 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.370 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9147 Z= 0.195 Angle : 0.568 5.760 12406 Z= 0.386 Chirality : 0.043 0.226 1401 Planarity : 0.003 0.046 1588 Dihedral : 14.485 89.621 3208 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.77 % Allowed : 8.96 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.23), residues: 1144 helix: 0.35 (0.23), residues: 459 sheet: -0.46 (0.32), residues: 232 loop : -1.40 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.000 HIS A 357 PHE 0.009 0.001 PHE A 212 TYR 0.011 0.001 TYR P 13 ARG 0.002 0.000 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 186 ASP cc_start: 0.7105 (m-30) cc_final: 0.6851 (m-30) outliers start: 7 outliers final: 3 residues processed: 164 average time/residue: 1.2747 time to fit residues: 222.3861 Evaluate side-chains 114 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 218 ASN A 254 ASN A 292 ASN B 36 ASN B 44 GLN B 175 GLN B 259 GLN B 268 ASN N 31 ASN N 77 ASN N 120 GLN R 410 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9147 Z= 0.142 Angle : 0.470 6.787 12406 Z= 0.257 Chirality : 0.039 0.138 1401 Planarity : 0.004 0.048 1588 Dihedral : 3.909 29.513 1273 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.65 % Allowed : 15.71 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1144 helix: 1.36 (0.24), residues: 468 sheet: -0.05 (0.33), residues: 237 loop : -0.66 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.009 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.013 0.001 TYR R 305 ARG 0.004 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.6349 (OUTLIER) cc_final: 0.5200 (mmt180) outliers start: 24 outliers final: 5 residues processed: 136 average time/residue: 1.3044 time to fit residues: 188.6476 Evaluate side-chains 121 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 390 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 213 GLN A 267 GLN A 292 ASN B 44 GLN B 110 ASN B 175 GLN B 268 ASN B 340 ASN N 1 GLN N 31 ASN N 77 ASN N 120 GLN R 410 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9147 Z= 0.319 Angle : 0.615 8.888 12406 Z= 0.335 Chirality : 0.045 0.146 1401 Planarity : 0.005 0.049 1588 Dihedral : 4.690 39.163 1270 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.43 % Allowed : 17.59 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1144 helix: 1.25 (0.24), residues: 463 sheet: 0.16 (0.33), residues: 241 loop : -0.50 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.014 0.002 HIS A 357 PHE 0.018 0.002 PHE B 151 TYR 0.018 0.002 TYR R 305 ARG 0.008 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 122 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.6476 (OUTLIER) cc_final: 0.5472 (mmt180) outliers start: 31 outliers final: 14 residues processed: 136 average time/residue: 1.3249 time to fit residues: 191.3758 Evaluate side-chains 130 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 418 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 50.0000 chunk 53 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 213 GLN B 44 GLN B 175 GLN B 268 ASN N 31 ASN N 39 GLN N 77 ASN N 120 GLN R 410 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9147 Z= 0.345 Angle : 0.632 9.246 12406 Z= 0.344 Chirality : 0.046 0.157 1401 Planarity : 0.005 0.048 1588 Dihedral : 4.949 45.504 1270 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.42 % Allowed : 17.59 % Favored : 77.99 % 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: 0.33 (0.24), residues: 1144 helix: 1.19 (0.24), residues: 463 sheet: 0.11 (0.33), residues: 232 loop : -0.67 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 234 HIS 0.010 0.002 HIS A 357 PHE 0.019 0.002 PHE B 151 TYR 0.021 0.003 TYR R 305 ARG 0.008 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 118 time to evaluate : 1.082 Fit side-chains REVERT: A 343 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.6385 (m-30) REVERT: B 42 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.5442 (mmp-170) REVERT: B 44 GLN cc_start: 0.6881 (OUTLIER) cc_final: 0.6672 (mp-120) REVERT: R 410 GLN cc_start: 0.6146 (mt0) cc_final: 0.5927 (mt0) outliers start: 40 outliers final: 16 residues processed: 144 average time/residue: 1.2732 time to fit residues: 195.1378 Evaluate side-chains 132 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain R residue 390 PHE Chi-restraints excluded: chain R residue 418 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 50.0000 chunk 45 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 357 HIS B 268 ASN B 340 ASN N 31 ASN N 77 ASN N 120 GLN R 304 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9147 Z= 0.343 Angle : 0.633 9.629 12406 Z= 0.344 Chirality : 0.046 0.157 1401 Planarity : 0.005 0.053 1588 Dihedral : 5.027 47.700 1270 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.98 % Allowed : 19.03 % Favored : 76.99 % 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: 0.35 (0.24), residues: 1144 helix: 1.23 (0.24), residues: 460 sheet: 0.15 (0.33), residues: 232 loop : -0.68 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 234 HIS 0.006 0.002 HIS B 311 PHE 0.020 0.002 PHE B 151 TYR 0.024 0.003 TYR R 305 ARG 0.006 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.113 Fit side-chains REVERT: B 42 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.5557 (mmt180) REVERT: B 155 ASN cc_start: 0.6471 (OUTLIER) cc_final: 0.6119 (t0) REVERT: R 410 GLN cc_start: 0.6199 (mt0) cc_final: 0.5981 (mt0) outliers start: 36 outliers final: 16 residues processed: 142 average time/residue: 1.2883 time to fit residues: 194.9186 Evaluate side-chains 131 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain R residue 418 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.0170 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.3420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 357 HIS B 44 GLN B 175 GLN B 268 ASN B 340 ASN N 31 ASN N 77 ASN N 120 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9147 Z= 0.186 Angle : 0.529 9.638 12406 Z= 0.288 Chirality : 0.041 0.142 1401 Planarity : 0.004 0.048 1588 Dihedral : 4.631 46.267 1270 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.87 % Allowed : 19.47 % Favored : 76.66 % 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: 0.85 (0.25), residues: 1144 helix: 1.71 (0.24), residues: 452 sheet: 0.38 (0.33), residues: 235 loop : -0.44 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 203 HIS 0.003 0.001 HIS B 54 PHE 0.015 0.001 PHE B 151 TYR 0.026 0.002 TYR R 305 ARG 0.004 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 114 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.5530 (mmt180) REVERT: B 59 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7461 (t80) REVERT: B 155 ASN cc_start: 0.6396 (OUTLIER) cc_final: 0.6068 (t0) REVERT: R 340 MET cc_start: 0.4375 (pmm) cc_final: 0.4053 (tpp) REVERT: R 410 GLN cc_start: 0.6103 (mt0) cc_final: 0.5895 (mt0) outliers start: 35 outliers final: 16 residues processed: 137 average time/residue: 1.2494 time to fit residues: 182.4245 Evaluate side-chains 131 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain R residue 418 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 80 optimal weight: 30.0000 chunk 92 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 357 HIS B 44 GLN B 268 ASN B 340 ASN N 31 ASN N 77 ASN N 120 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9147 Z= 0.209 Angle : 0.551 9.773 12406 Z= 0.297 Chirality : 0.042 0.145 1401 Planarity : 0.004 0.048 1588 Dihedral : 4.637 44.842 1270 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.98 % Allowed : 19.58 % Favored : 76.44 % 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: 0.90 (0.25), residues: 1144 helix: 1.72 (0.24), residues: 458 sheet: 0.40 (0.33), residues: 236 loop : -0.41 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 203 HIS 0.004 0.001 HIS B 54 PHE 0.017 0.001 PHE B 151 TYR 0.024 0.002 TYR R 305 ARG 0.004 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 116 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.5544 (mmt180) REVERT: B 59 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7457 (t80) REVERT: B 155 ASN cc_start: 0.6437 (OUTLIER) cc_final: 0.6092 (t0) REVERT: R 410 GLN cc_start: 0.6119 (mt0) cc_final: 0.5908 (mt0) outliers start: 36 outliers final: 21 residues processed: 139 average time/residue: 1.2753 time to fit residues: 188.8391 Evaluate side-chains 136 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 362 THR Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain R residue 418 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 69 optimal weight: 6.9990 chunk 74 optimal weight: 50.0000 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 357 HIS B 44 GLN B 268 ASN B 340 ASN N 31 ASN N 77 ASN N 120 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9147 Z= 0.142 Angle : 0.504 9.800 12406 Z= 0.271 Chirality : 0.040 0.146 1401 Planarity : 0.004 0.047 1588 Dihedral : 4.308 40.014 1270 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.10 % Allowed : 20.91 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1144 helix: 1.91 (0.25), residues: 460 sheet: 0.68 (0.34), residues: 222 loop : -0.38 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 203 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.021 0.001 TYR R 305 ARG 0.003 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 0.973 Fit side-chains REVERT: B 42 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.5415 (mmt180) REVERT: B 59 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7497 (t80) REVERT: B 155 ASN cc_start: 0.6390 (OUTLIER) cc_final: 0.6064 (t0) outliers start: 28 outliers final: 12 residues processed: 130 average time/residue: 1.2969 time to fit residues: 179.2742 Evaluate side-chains 125 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 80 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 chunk 92 optimal weight: 0.0030 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 357 HIS B 44 GLN B 268 ASN B 340 ASN N 77 ASN N 120 GLN R 410 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9147 Z= 0.230 Angle : 0.574 10.032 12406 Z= 0.307 Chirality : 0.042 0.149 1401 Planarity : 0.004 0.049 1588 Dihedral : 4.612 39.470 1270 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.54 % Allowed : 20.80 % Favored : 75.66 % 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: 1.09 (0.25), residues: 1144 helix: 1.91 (0.24), residues: 452 sheet: 0.54 (0.33), residues: 234 loop : -0.33 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 203 HIS 0.005 0.001 HIS B 54 PHE 0.017 0.002 PHE B 151 TYR 0.022 0.002 TYR R 305 ARG 0.005 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 1.063 Fit side-chains REVERT: B 42 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.5545 (mmt180) REVERT: B 155 ASN cc_start: 0.6464 (OUTLIER) cc_final: 0.6119 (t0) REVERT: R 340 MET cc_start: 0.4046 (pmm) cc_final: 0.3819 (tpp) outliers start: 32 outliers final: 16 residues processed: 132 average time/residue: 1.3306 time to fit residues: 188.1603 Evaluate side-chains 129 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 171 HIS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 chunk 113 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN A 357 HIS B 44 GLN B 268 ASN B 340 ASN N 77 ASN N 120 GLN R 410 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9147 Z= 0.173 Angle : 0.531 9.569 12406 Z= 0.286 Chirality : 0.041 0.150 1401 Planarity : 0.004 0.048 1588 Dihedral : 4.419 36.197 1270 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.65 % Allowed : 22.35 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1144 helix: 1.96 (0.25), residues: 458 sheet: 0.58 (0.33), residues: 233 loop : -0.32 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 264 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.018 0.001 TYR R 305 ARG 0.005 0.000 ARG A 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 1.133 Fit side-chains REVERT: B 42 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.5413 (mmt180) REVERT: B 59 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7459 (t80) REVERT: B 155 ASN cc_start: 0.6390 (OUTLIER) cc_final: 0.6054 (t0) outliers start: 24 outliers final: 14 residues processed: 128 average time/residue: 1.2821 time to fit residues: 174.5114 Evaluate side-chains 126 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 314 LEU Chi-restraints excluded: chain R residue 362 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 65 optimal weight: 0.0570 overall best weight: 2.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 54 ASN B 44 GLN B 268 ASN B 340 ASN N 77 ASN N 120 GLN R 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.188721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.131693 restraints weight = 10473.947| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.88 r_work: 0.3578 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9147 Z= 0.295 Angle : 0.612 9.994 12406 Z= 0.330 Chirality : 0.044 0.153 1401 Planarity : 0.005 0.048 1588 Dihedral : 4.824 41.067 1270 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.99 % Allowed : 21.90 % Favored : 75.11 % 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: 0.81 (0.25), residues: 1144 helix: 1.67 (0.24), residues: 464 sheet: 0.39 (0.33), residues: 238 loop : -0.54 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP R 264 HIS 0.011 0.002 HIS A 357 PHE 0.019 0.002 PHE B 151 TYR 0.018 0.002 TYR R 242 ARG 0.007 0.001 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4564.65 seconds wall clock time: 387 minutes 33.14 seconds (23253.14 seconds total)