Starting phenix.real_space_refine on Tue Nov 14 15:44:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/11_2023/7rtb_24680_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/11_2023/7rtb_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_24680/11_2023/7rtb_24680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/11_2023/7rtb_24680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/11_2023/7rtb_24680_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtb_24680/11_2023/7rtb_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-1.21rc1-5144/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: 5.43, 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: 3.51 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: 1.89 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: 2.70 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 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: 1.930 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: 7.280 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.350 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.530 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 164 average time/residue: 1.2850 time to fit residues: 223.8509 Evaluate side-chains 114 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.2871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.6800 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9147 Z= 0.144 Angle : 0.472 6.763 12406 Z= 0.258 Chirality : 0.039 0.137 1401 Planarity : 0.004 0.048 1588 Dihedral : 3.718 23.603 1269 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.77 % Allowed : 15.82 % Favored : 81.42 % 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: 0.42 (0.24), residues: 1144 helix: 1.36 (0.24), residues: 468 sheet: -0.02 (0.33), residues: 236 loop : -0.66 (0.28), residues: 440 *********************** 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: 25 poor density : 124 time to evaluate : 1.078 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 7 residues processed: 136 average time/residue: 1.3301 time to fit residues: 192.3592 Evaluate side-chains 121 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 2 average time/residue: 0.9502 time to fit residues: 3.5256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9147 Z= 0.301 Angle : 0.612 8.710 12406 Z= 0.333 Chirality : 0.045 0.146 1401 Planarity : 0.005 0.048 1588 Dihedral : 4.591 27.640 1269 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.21 % Allowed : 17.70 % Favored : 79.09 % 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: 0.50 (0.25), residues: 1144 helix: 1.27 (0.24), residues: 462 sheet: 0.25 (0.33), residues: 235 loop : -0.53 (0.29), residues: 447 *********************** 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: 29 poor density : 124 time to evaluate : 0.921 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 139 average time/residue: 1.3760 time to fit residues: 202.8679 Evaluate side-chains 130 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.1653 time to fit residues: 1.9996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.6980 chunk 77 optimal weight: 50.0000 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 110 ASN B 268 ASN N 31 ASN N 39 GLN N 77 ASN N 120 GLN R 304 ASN R 410 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9147 Z= 0.359 Angle : 0.654 9.455 12406 Z= 0.355 Chirality : 0.047 0.157 1401 Planarity : 0.006 0.053 1588 Dihedral : 4.851 23.572 1269 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.76 % Allowed : 17.26 % 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: 0.39 (0.24), residues: 1144 helix: 1.24 (0.24), residues: 459 sheet: 0.15 (0.33), residues: 232 loop : -0.62 (0.28), residues: 453 *********************** 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 157 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 114 time to evaluate : 1.290 Fit side-chains outliers start: 43 outliers final: 17 residues processed: 145 average time/residue: 1.3002 time to fit residues: 201.1153 Evaluate side-chains 128 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.429 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.0872 time to fit residues: 1.8388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 50.0000 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 0.0980 chunk 76 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- 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 A 357 HIS B 268 ASN N 31 ASN N 77 ASN N 120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9147 Z= 0.383 Angle : 0.666 9.555 12406 Z= 0.363 Chirality : 0.048 0.279 1401 Planarity : 0.006 0.050 1588 Dihedral : 4.995 23.724 1269 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.20 % Allowed : 18.36 % Favored : 77.43 % 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: 0.23 (0.24), residues: 1144 helix: 1.08 (0.24), residues: 465 sheet: 0.13 (0.33), residues: 233 loop : -0.75 (0.28), residues: 446 *********************** 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 156 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 118 time to evaluate : 1.130 Fit side-chains outliers start: 38 outliers final: 17 residues processed: 148 average time/residue: 1.2749 time to fit residues: 201.3731 Evaluate side-chains 131 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.0838 time to fit residues: 1.6345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 N 31 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: 0.6975 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9147 Z= 0.218 Angle : 0.555 9.659 12406 Z= 0.302 Chirality : 0.042 0.237 1401 Planarity : 0.004 0.050 1588 Dihedral : 4.608 23.322 1269 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.20 % Allowed : 19.03 % Favored : 76.77 % 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: 0.72 (0.25), residues: 1144 helix: 1.60 (0.24), residues: 452 sheet: 0.36 (0.34), residues: 231 loop : -0.54 (0.29), residues: 461 *********************** 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 155 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 117 time to evaluate : 1.050 Fit side-chains outliers start: 38 outliers final: 19 residues processed: 141 average time/residue: 1.3721 time to fit residues: 206.6563 Evaluate side-chains 132 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 0.1233 time to fit residues: 2.1740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.0670 chunk 12 optimal weight: 0.0870 chunk 62 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- 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 155 ASN B 268 ASN N 31 ASN N 77 ASN N 120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9147 Z= 0.158 Angle : 0.515 9.771 12406 Z= 0.278 Chirality : 0.041 0.222 1401 Planarity : 0.004 0.047 1588 Dihedral : 4.279 22.168 1269 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.54 % Allowed : 19.91 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1144 helix: 1.84 (0.25), residues: 458 sheet: 0.67 (0.34), residues: 223 loop : -0.50 (0.29), residues: 463 *********************** 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 148 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 0.975 Fit side-chains outliers start: 32 outliers final: 21 residues processed: 139 average time/residue: 1.5225 time to fit residues: 225.1917 Evaluate side-chains 132 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.6694 time to fit residues: 3.6917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 40.0000 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 N 31 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: 0.6979 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9147 Z= 0.245 Angle : 0.579 9.882 12406 Z= 0.313 Chirality : 0.043 0.205 1401 Planarity : 0.004 0.048 1588 Dihedral : 4.547 22.920 1269 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.20 % Allowed : 19.91 % Favored : 75.88 % 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: 0.97 (0.25), residues: 1144 helix: 1.86 (0.24), residues: 452 sheet: 0.45 (0.34), residues: 231 loop : -0.43 (0.29), residues: 461 *********************** 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 151 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 113 time to evaluate : 1.119 Fit side-chains outliers start: 38 outliers final: 23 residues processed: 139 average time/residue: 1.3266 time to fit residues: 196.1240 Evaluate side-chains 136 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 4 average time/residue: 0.3545 time to fit residues: 2.9331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 105 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 N 31 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: 0.6961 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9147 Z= 0.209 Angle : 0.561 9.837 12406 Z= 0.302 Chirality : 0.042 0.195 1401 Planarity : 0.004 0.048 1588 Dihedral : 4.462 22.826 1269 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.65 % Allowed : 21.68 % 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: 1.00 (0.25), residues: 1144 helix: 1.88 (0.24), residues: 458 sheet: 0.51 (0.34), residues: 230 loop : -0.46 (0.30), residues: 456 *********************** 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 133 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 1.060 Fit side-chains outliers start: 24 outliers final: 19 residues processed: 130 average time/residue: 1.3140 time to fit residues: 181.7945 Evaluate side-chains 127 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 0 time to fit residues: 1.3317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 113 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 N 31 ASN N 77 ASN N 120 GLN R 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9147 Z= 0.202 Angle : 0.554 10.466 12406 Z= 0.298 Chirality : 0.042 0.187 1401 Planarity : 0.004 0.048 1588 Dihedral : 4.445 22.686 1269 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.88 % Allowed : 21.79 % Favored : 75.33 % 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: 1.02 (0.25), residues: 1144 helix: 1.94 (0.25), residues: 456 sheet: 0.51 (0.34), residues: 230 loop : -0.49 (0.29), residues: 458 ********************** 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 137 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.065 Fit side-chains outliers start: 26 outliers final: 21 residues processed: 131 average time/residue: 1.3509 time to fit residues: 188.5874 Evaluate side-chains 131 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.5565 time to fit residues: 2.6444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.0870 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.3960 ------------------------------------------------------------------------------- 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 N 31 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 = 0.4413 r_free = 0.4413 target = 0.190385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.133796 restraints weight = 10421.023| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.88 r_work: 0.3607 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3842 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= 0.187 Angle : 0.540 9.906 12406 Z= 0.292 Chirality : 0.041 0.184 1401 Planarity : 0.004 0.048 1588 Dihedral : 4.390 22.507 1269 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.77 % Allowed : 22.01 % Favored : 75.22 % 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: 2.05 (0.25), residues: 456 sheet: 0.58 (0.34), residues: 229 loop : -0.47 (0.29), residues: 459 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4476.00 seconds wall clock time: 79 minutes 42.17 seconds (4782.17 seconds total)