Starting phenix.real_space_refine on Fri Sep 11 15:07:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xhy_66890/09_2026/9xhy_66890.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xhy_66890/09_2026/9xhy_66890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xhy_66890/09_2026/9xhy_66890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xhy_66890/09_2026/9xhy_66890.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xhy_66890/09_2026/9xhy_66890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xhy_66890/09_2026/9xhy_66890.map" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.025 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 50 5.16 5 C 6149 2.51 5 N 1608 2.21 5 O 1868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9676 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4864 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1540 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "H" Number of atoms: 1645 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 222, 1641 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 210} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 222, 1641 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 210} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1671 Chain: "L" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1570 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 196} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.38, per 1000 atoms: 0.25 Number of scatterers: 9676 At special positions: 0 Unit cell: (77.55, 113.85, 151.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 50 16.00 O 1868 8.00 N 1608 7.00 C 6149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 207 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 902 " - " ASN A 53 " " NAG A 903 " - " ASN A 90 " " NAG A 904 " - " ASN A 322 " " NAG A 905 " - " ASN A 546 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 402.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2284 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 39.2% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.841A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.521A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.659A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.824A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.763A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 removed outlier: 4.245A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 283 removed outlier: 4.666A pdb=" N SER A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A 283 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.664A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.667A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.505A pdb=" N LEU A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.607A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.595A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.653A pdb=" N SER A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.302A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.571A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 364 through 371 removed outlier: 3.593A pdb=" N ASN E 370 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.462A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.713A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.617A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.684A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 202 removed outlier: 3.586A pdb=" N GLY H 201 " --> pdb=" O SER H 198 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR H 202 " --> pdb=" O SER H 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 198 through 202' Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'L' and resid 128 through 133 Processing helix chain 'L' and resid 186 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.869A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.289A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.586A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.745A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'E' and resid 466 through 467 Processing sheet with id=AA8, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.783A pdb=" N GLU H 82 " --> pdb=" O MET H 69 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET H 69 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.314A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.975A pdb=" N CYS H 96 " --> pdb=" O TRP H 114 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TRP H 114 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG H 98 " --> pdb=" O ASP H 112 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR H 110 " --> pdb=" O SER H 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.516A pdb=" N LYS H 154 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL H 192 " --> pdb=" O HIS H 175 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS H 175 " --> pdb=" O VAL H 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 131 through 135 removed outlier: 3.516A pdb=" N LYS H 154 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY H 150 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU H 149 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR H 187 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 162 through 165 removed outlier: 3.571A pdb=" N THR H 162 " --> pdb=" O ASN H 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.793A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA L 86 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.793A pdb=" N VAL L 10 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA L 86 " --> pdb=" O VAL L 108 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB9, first strand: chain 'L' and resid 121 through 122 removed outlier: 3.772A pdb=" N ALA L 135 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER L 181 " --> pdb=" O CYS L 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 121 through 122 Processing sheet with id=AC2, first strand: chain 'L' and resid 150 through 154 removed outlier: 3.791A pdb=" N THR L 150 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS L 209 " --> pdb=" O CYS L 198 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1176 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: 1.58 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3063 1.34 - 1.46: 2202 1.46 - 1.58: 4595 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 9938 Sorted by residual: bond pdb=" C TYR L 145 " pdb=" N PRO L 146 " ideal model delta sigma weight residual 1.337 1.373 -0.036 9.80e-03 1.04e+04 1.39e+01 bond pdb=" N MET A 323 " pdb=" CA MET A 323 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.47e+00 bond pdb=" N THR A 324 " pdb=" CA THR A 324 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.21e-02 6.83e+03 6.38e+00 bond pdb=" N ASN A 90 " pdb=" CA ASN A 90 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.24e-02 6.50e+03 6.06e+00 bond pdb=" N SER L 192 " pdb=" CA SER L 192 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.28e-02 6.10e+03 5.47e+00 ... (remaining 9933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 13456 3.54 - 7.08: 65 7.08 - 10.62: 5 10.62 - 14.15: 2 14.15 - 17.69: 1 Bond angle restraints: 13529 Sorted by residual: angle pdb=" O GLY L 112 " pdb=" C GLY L 112 " pdb=" N GLN L 113 " ideal model delta sigma weight residual 122.70 105.01 17.69 1.30e+00 5.92e-01 1.85e+02 angle pdb=" CB MET H 69 " pdb=" CG MET H 69 " pdb=" SD MET H 69 " ideal model delta sigma weight residual 112.70 123.95 -11.25 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CB MET A 474 " pdb=" CG MET A 474 " pdb=" SD MET A 474 " ideal model delta sigma weight residual 112.70 123.75 -11.05 3.00e+00 1.11e-01 1.36e+01 angle pdb=" C THR H 30 " pdb=" N ASN H 31 " pdb=" CA ASN H 31 " ideal model delta sigma weight residual 121.54 128.57 -7.03 1.91e+00 2.74e-01 1.35e+01 angle pdb=" N LYS A 234 " pdb=" CA LYS A 234 " pdb=" C LYS A 234 " ideal model delta sigma weight residual 113.45 118.39 -4.94 1.39e+00 5.18e-01 1.26e+01 ... (remaining 13524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 5369 17.58 - 35.15: 475 35.15 - 52.73: 66 52.73 - 70.31: 22 70.31 - 87.89: 13 Dihedral angle restraints: 5945 sinusoidal: 2373 harmonic: 3572 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 62.33 30.67 1 1.00e+01 1.00e-02 1.34e+01 dihedral pdb=" CA ASP E 339 " pdb=" CB ASP E 339 " pdb=" CG ASP E 339 " pdb=" OD1 ASP E 339 " ideal model delta sinusoidal sigma weight residual -30.00 -89.82 59.82 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 121.07 -28.07 1 1.00e+01 1.00e-02 1.13e+01 ... (remaining 5942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 971 0.039 - 0.079: 320 0.079 - 0.118: 139 0.118 - 0.158: 33 0.158 - 0.197: 4 Chirality restraints: 1467 Sorted by residual: chirality pdb=" CA LEU A 143 " pdb=" N LEU A 143 " pdb=" C LEU A 143 " pdb=" CB LEU A 143 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CA ASN H 31 " pdb=" N ASN H 31 " pdb=" C ASN H 31 " pdb=" CB ASN H 31 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CA LYS A 234 " pdb=" N LYS A 234 " pdb=" C LYS A 234 " pdb=" CB LYS A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 1464 not shown) Planarity restraints: 1749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 112 " 0.084 2.00e-02 2.50e+03 1.52e-01 2.31e+02 pdb=" C GLY L 112 " -0.263 2.00e-02 2.50e+03 pdb=" O GLY L 112 " 0.096 2.00e-02 2.50e+03 pdb=" N GLN L 113 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 903 " 0.080 2.00e-02 2.50e+03 6.59e-02 5.43e+01 pdb=" C7 NAG A 903 " -0.027 2.00e-02 2.50e+03 pdb=" C8 NAG A 903 " 0.062 2.00e-02 2.50e+03 pdb=" N2 NAG A 903 " -0.103 2.00e-02 2.50e+03 pdb=" O7 NAG A 903 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 353 " -0.014 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP E 353 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP E 353 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP E 353 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 353 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP E 353 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 353 " -0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 353 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 353 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 353 " 0.001 2.00e-02 2.50e+03 ... (remaining 1746 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1690 2.77 - 3.30: 8920 3.30 - 3.83: 16175 3.83 - 4.37: 18235 4.37 - 4.90: 32404 Nonbonded interactions: 77424 Sorted by model distance: nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR E 500 " model vdw 2.292 3.040 nonbonded pdb=" OG1 THR A 276 " pdb=" OG1 THR A 445 " model vdw 2.306 3.040 nonbonded pdb=" OG SER A 109 " pdb=" OD1 ASP A 111 " model vdw 2.312 3.040 nonbonded pdb=" NE2 GLN L 91 " pdb=" OG SER L 100 " model vdw 2.316 3.120 ... (remaining 77419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.270 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 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 : 0.004 0.055 9955 Z= 0.210 Angle : 0.722 17.693 13565 Z= 0.382 Chirality : 0.048 0.197 1467 Planarity : 0.006 0.152 1745 Dihedral : 13.778 87.887 3625 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.23), residues: 1218 helix: 0.41 (0.24), residues: 396 sheet: 0.70 (0.33), residues: 252 loop : -0.43 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 460 TYR 0.016 0.002 TYR A 385 PHE 0.016 0.002 PHE L 144 TRP 0.054 0.002 TRP E 353 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 ( 9938) covalent geometry : angle 0.72011 / 0.38 (13529) SS BOND : bond 0.00212 / 0.14 ( 11) SS BOND : angle 0.73906 / 0.41 ( 24) hydrogen bonds : bond 0.20810 / 14.21 ( 417) hydrogen bonds : angle 7.38543 / 5.22 ( 1176) metal coordination : bond 0.00221 / 0.11 ( 2) link_NAG-ASN : bond 0.00539 / 0.25 ( 4) link_NAG-ASN : angle 1.83259 / 1.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 474 MET cc_start: 0.8358 (mmp) cc_final: 0.8061 (mmp) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0875 time to fit residues: 5.7133 Evaluate side-chains 41 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0570 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 133 ASN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.064632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.051768 restraints weight = 41367.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.053513 restraints weight = 23100.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.054657 restraints weight = 15997.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.055408 restraints weight = 12577.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.055895 restraints weight = 10704.500| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9955 Z= 0.123 Angle : 0.511 7.123 13565 Z= 0.262 Chirality : 0.042 0.142 1467 Planarity : 0.003 0.033 1745 Dihedral : 4.298 50.187 1409 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.66 % Allowed : 5.12 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.24), residues: 1218 helix: 1.37 (0.26), residues: 404 sheet: 0.67 (0.31), residues: 264 loop : -0.16 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.012 0.001 TYR A 41 PHE 0.013 0.001 PHE E 400 TRP 0.020 0.001 TRP E 353 HIS 0.005 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9938) covalent geometry : angle 0.50821 / 0.26 (13529) SS BOND : bond 0.00351 / 0.19 ( 11) SS BOND : angle 0.73099 / 0.35 ( 24) hydrogen bonds : bond 0.04010 / 2.68 ( 417) hydrogen bonds : angle 4.99088 / 3.49 ( 1176) metal coordination : bond 0.00118 / 0.06 ( 2) link_NAG-ASN : bond 0.00107 / 0.05 ( 4) link_NAG-ASN : angle 1.58178 / 0.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: E 364 ASP cc_start: 0.7799 (t0) cc_final: 0.7568 (t0) outliers start: 7 outliers final: 3 residues processed: 46 average time/residue: 0.0938 time to fit residues: 6.6582 Evaluate side-chains 41 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain L residue 51 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 0 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 105 optimal weight: 0.2980 chunk 44 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 0.0170 chunk 110 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.065349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.052530 restraints weight = 41177.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.054323 restraints weight = 22835.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.055477 restraints weight = 15750.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.056255 restraints weight = 12326.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.056744 restraints weight = 10453.622| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9955 Z= 0.092 Angle : 0.478 7.222 13565 Z= 0.239 Chirality : 0.041 0.146 1467 Planarity : 0.003 0.030 1745 Dihedral : 3.815 37.788 1409 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.76 % Allowed : 6.26 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.25), residues: 1218 helix: 1.79 (0.26), residues: 404 sheet: 0.81 (0.32), residues: 253 loop : -0.18 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.010 0.001 TYR A 158 PHE 0.009 0.001 PHE L 144 TRP 0.010 0.001 TRP A 168 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 ( 9938) covalent geometry : angle 0.47705 / 0.24 (13529) SS BOND : bond 0.00200 / 0.12 ( 11) SS BOND : angle 0.43493 / 0.21 ( 24) hydrogen bonds : bond 0.03369 / 2.26 ( 417) hydrogen bonds : angle 4.43773 / 3.10 ( 1176) metal coordination : bond 0.00037 / 0.02 ( 2) link_NAG-ASN : bond 0.00169 / 0.07 ( 4) link_NAG-ASN : angle 1.33603 / 0.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: H 81 MET cc_start: 0.8626 (tmm) cc_final: 0.7814 (tmm) outliers start: 8 outliers final: 4 residues processed: 45 average time/residue: 0.0857 time to fit residues: 6.0219 Evaluate side-chains 43 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain L residue 160 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 14 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 chunk 68 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.065763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.052922 restraints weight = 41458.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.054712 restraints weight = 23217.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.055886 restraints weight = 16037.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.056643 restraints weight = 12571.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.057160 restraints weight = 10648.445| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9955 Z= 0.091 Angle : 0.472 7.206 13565 Z= 0.235 Chirality : 0.041 0.146 1467 Planarity : 0.003 0.030 1745 Dihedral : 3.520 21.700 1409 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.76 % Allowed : 6.83 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.25), residues: 1218 helix: 1.96 (0.27), residues: 404 sheet: 0.85 (0.33), residues: 253 loop : -0.12 (0.28), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 87 TYR 0.009 0.001 TYR A 158 PHE 0.009 0.001 PHE A 230 TRP 0.009 0.001 TRP A 168 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.09 ( 9938) covalent geometry : angle 0.47103 / 0.23 (13529) SS BOND : bond 0.00170 / 0.11 ( 11) SS BOND : angle 0.41274 / 0.20 ( 24) hydrogen bonds : bond 0.03106 / 2.10 ( 417) hydrogen bonds : angle 4.23575 / 2.96 ( 1176) metal coordination : bond 0.00059 / 0.03 ( 2) link_NAG-ASN : bond 0.00190 / 0.08 ( 4) link_NAG-ASN : angle 1.21833 / 0.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.385 Fit side-chains REVERT: H 81 MET cc_start: 0.8609 (tmm) cc_final: 0.8044 (tmm) REVERT: L 191 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8916 (mmmt) outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 0.0916 time to fit residues: 5.8510 Evaluate side-chains 43 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain L residue 160 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 119 optimal weight: 0.0050 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 0.1980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.065573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.052733 restraints weight = 41522.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.054500 restraints weight = 23140.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.055666 restraints weight = 16009.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.056428 restraints weight = 12552.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.056897 restraints weight = 10666.080| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9955 Z= 0.093 Angle : 0.470 7.333 13565 Z= 0.233 Chirality : 0.040 0.146 1467 Planarity : 0.003 0.029 1745 Dihedral : 3.383 14.757 1409 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.66 % Allowed : 7.97 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.25), residues: 1218 helix: 2.04 (0.27), residues: 404 sheet: 0.87 (0.33), residues: 253 loop : -0.10 (0.28), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.009 0.001 TYR A 237 PHE 0.009 0.001 PHE A 230 TRP 0.008 0.001 TRP A 168 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 9938) covalent geometry : angle 0.46907 / 0.23 (13529) SS BOND : bond 0.00163 / 0.11 ( 11) SS BOND : angle 0.35721 / 0.18 ( 24) hydrogen bonds : bond 0.03043 / 2.06 ( 417) hydrogen bonds : angle 4.11835 / 2.88 ( 1176) metal coordination : bond 0.00063 / 0.03 ( 2) link_NAG-ASN : bond 0.00158 / 0.07 ( 4) link_NAG-ASN : angle 1.20966 / 0.74 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.339 Fit side-chains REVERT: H 81 MET cc_start: 0.8472 (tmm) cc_final: 0.7908 (tmm) REVERT: L 191 LYS cc_start: 0.9164 (mmmt) cc_final: 0.8927 (mmmt) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 0.0848 time to fit residues: 5.8719 Evaluate side-chains 45 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain L residue 160 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 118 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 95 optimal weight: 0.0000 chunk 50 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN H 6 GLN ** H 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.065330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.052437 restraints weight = 41455.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.054214 restraints weight = 23045.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.055366 restraints weight = 15890.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.056128 restraints weight = 12449.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.056611 restraints weight = 10600.877| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9955 Z= 0.101 Angle : 0.480 6.963 13565 Z= 0.238 Chirality : 0.041 0.144 1467 Planarity : 0.003 0.029 1745 Dihedral : 3.345 14.567 1409 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.80 % Favored : 97.12 % Rotamer: Outliers : 0.76 % Allowed : 8.25 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.25), residues: 1218 helix: 2.05 (0.27), residues: 404 sheet: 0.98 (0.33), residues: 247 loop : -0.05 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.010 0.001 TYR A 237 PHE 0.009 0.001 PHE A 230 TRP 0.008 0.001 TRP A 168 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 9938) covalent geometry : angle 0.47947 / 0.24 (13529) SS BOND : bond 0.00169 / 0.11 ( 11) SS BOND : angle 0.34230 / 0.17 ( 24) hydrogen bonds : bond 0.03019 / 2.06 ( 417) hydrogen bonds : angle 4.06340 / 2.83 ( 1176) metal coordination : bond 0.00078 / 0.04 ( 2) link_NAG-ASN : bond 0.00157 / 0.07 ( 4) link_NAG-ASN : angle 1.19762 / 0.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.335 Fit side-chains REVERT: A 474 MET cc_start: 0.8312 (mmp) cc_final: 0.7938 (mmp) REVERT: E 342 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7898 (m-10) REVERT: H 81 MET cc_start: 0.8453 (tmm) cc_final: 0.7897 (tmm) REVERT: L 191 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8950 (mmmt) outliers start: 8 outliers final: 6 residues processed: 45 average time/residue: 0.0853 time to fit residues: 5.9833 Evaluate side-chains 47 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain L residue 160 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.064706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.051777 restraints weight = 41341.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.053504 restraints weight = 23315.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.054661 restraints weight = 16231.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.055403 restraints weight = 12788.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.055884 restraints weight = 10892.930| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9955 Z= 0.124 Angle : 0.496 7.626 13565 Z= 0.246 Chirality : 0.041 0.143 1467 Planarity : 0.003 0.028 1745 Dihedral : 3.392 14.467 1409 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.80 % Favored : 97.12 % Rotamer: Outliers : 0.95 % Allowed : 7.97 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.25), residues: 1218 helix: 2.02 (0.27), residues: 404 sheet: 1.03 (0.33), residues: 247 loop : -0.05 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.013 0.001 TYR A 237 PHE 0.010 0.001 PHE A 230 TRP 0.007 0.001 TRP A 168 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 9938) covalent geometry : angle 0.49533 / 0.25 (13529) SS BOND : bond 0.00177 / 0.12 ( 11) SS BOND : angle 0.36793 / 0.19 ( 24) hydrogen bonds : bond 0.03162 / 2.16 ( 417) hydrogen bonds : angle 4.08688 / 2.85 ( 1176) metal coordination : bond 0.00120 / 0.06 ( 2) link_NAG-ASN : bond 0.00152 / 0.07 ( 4) link_NAG-ASN : angle 1.23248 / 0.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.375 Fit side-chains REVERT: E 342 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7902 (m-10) REVERT: H 81 MET cc_start: 0.8447 (tmm) cc_final: 0.7842 (tmm) REVERT: L 191 LYS cc_start: 0.9158 (mmmt) cc_final: 0.8939 (mmmt) outliers start: 10 outliers final: 6 residues processed: 46 average time/residue: 0.0832 time to fit residues: 5.8531 Evaluate side-chains 47 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain L residue 160 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 106 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.065141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.052296 restraints weight = 41181.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.054052 restraints weight = 22937.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.055199 restraints weight = 15845.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.055961 restraints weight = 12441.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.056413 restraints weight = 10547.024| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9955 Z= 0.097 Angle : 0.482 7.436 13565 Z= 0.238 Chirality : 0.041 0.141 1467 Planarity : 0.003 0.028 1745 Dihedral : 3.328 14.349 1409 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.80 % Favored : 97.12 % Rotamer: Outliers : 0.66 % Allowed : 8.63 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.25), residues: 1218 helix: 1.99 (0.26), residues: 405 sheet: 0.98 (0.33), residues: 247 loop : -0.04 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.009 0.001 TYR A 237 PHE 0.009 0.001 PHE A 230 TRP 0.008 0.001 TRP A 168 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 9938) covalent geometry : angle 0.48115 / 0.24 (13529) SS BOND : bond 0.00143 / 0.09 ( 11) SS BOND : angle 0.32276 / 0.16 ( 24) hydrogen bonds : bond 0.03044 / 2.08 ( 417) hydrogen bonds : angle 4.03549 / 2.82 ( 1176) metal coordination : bond 0.00072 / 0.03 ( 2) link_NAG-ASN : bond 0.00176 / 0.08 ( 4) link_NAG-ASN : angle 1.16815 / 0.72 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.351 Fit side-chains REVERT: E 342 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7861 (m-10) REVERT: H 81 MET cc_start: 0.8409 (tmm) cc_final: 0.7901 (tmm) REVERT: L 191 LYS cc_start: 0.9187 (mmmt) cc_final: 0.8975 (mmmt) outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 0.0858 time to fit residues: 5.8565 Evaluate side-chains 45 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain L residue 160 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 107 optimal weight: 0.0030 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 95 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 27 optimal weight: 0.0770 overall best weight: 0.5150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.065314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.052504 restraints weight = 41217.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.054249 restraints weight = 23185.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.055412 restraints weight = 16088.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.056143 restraints weight = 12621.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.056624 restraints weight = 10749.530| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9955 Z= 0.096 Angle : 0.478 7.857 13565 Z= 0.237 Chirality : 0.041 0.140 1467 Planarity : 0.003 0.028 1745 Dihedral : 3.317 14.968 1409 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.88 % Favored : 97.04 % Rotamer: Outliers : 0.76 % Allowed : 8.73 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.25), residues: 1218 helix: 2.04 (0.26), residues: 405 sheet: 0.98 (0.33), residues: 247 loop : -0.01 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.009 0.001 TYR A 237 PHE 0.009 0.001 PHE A 230 TRP 0.008 0.001 TRP A 168 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 9938) covalent geometry : angle 0.47674 / 0.24 (13529) SS BOND : bond 0.00146 / 0.10 ( 11) SS BOND : angle 0.33455 / 0.17 ( 24) hydrogen bonds : bond 0.02973 / 2.03 ( 417) hydrogen bonds : angle 3.97476 / 2.78 ( 1176) metal coordination : bond 0.00086 / 0.04 ( 2) link_NAG-ASN : bond 0.00152 / 0.07 ( 4) link_NAG-ASN : angle 1.15032 / 0.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.383 Fit side-chains REVERT: E 342 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7919 (m-10) REVERT: H 81 MET cc_start: 0.8377 (tmm) cc_final: 0.7890 (tmm) outliers start: 8 outliers final: 5 residues processed: 44 average time/residue: 0.0922 time to fit residues: 6.3239 Evaluate side-chains 45 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain L residue 160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 84 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 100 optimal weight: 0.0570 chunk 95 optimal weight: 3.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.065121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.052299 restraints weight = 41249.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.054037 restraints weight = 23204.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.055202 restraints weight = 16127.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.055922 restraints weight = 12663.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.056405 restraints weight = 10803.197| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9955 Z= 0.105 Angle : 0.493 8.172 13565 Z= 0.245 Chirality : 0.041 0.140 1467 Planarity : 0.003 0.029 1745 Dihedral : 3.355 14.945 1409 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.71 % Favored : 97.20 % Rotamer: Outliers : 0.66 % Allowed : 9.01 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.25), residues: 1218 helix: 2.00 (0.26), residues: 405 sheet: 1.01 (0.33), residues: 247 loop : 0.01 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.010 0.001 TYR A 237 PHE 0.010 0.001 PHE A 230 TRP 0.008 0.001 TRP A 168 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 9938) covalent geometry : angle 0.49218 / 0.24 (13529) SS BOND : bond 0.00148 / 0.10 ( 11) SS BOND : angle 0.33572 / 0.17 ( 24) hydrogen bonds : bond 0.03027 / 2.07 ( 417) hydrogen bonds : angle 3.96482 / 2.78 ( 1176) metal coordination : bond 0.00075 / 0.04 ( 2) link_NAG-ASN : bond 0.00162 / 0.07 ( 4) link_NAG-ASN : angle 1.11673 / 0.68 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.370 Fit side-chains REVERT: E 342 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7874 (m-10) REVERT: H 81 MET cc_start: 0.8397 (tmm) cc_final: 0.7916 (tmm) outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 0.0934 time to fit residues: 6.3684 Evaluate side-chains 47 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain L residue 160 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 0.0970 chunk 112 optimal weight: 0.8980 chunk 91 optimal weight: 0.1980 chunk 65 optimal weight: 0.0980 chunk 101 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.065723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053016 restraints weight = 40999.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.054712 restraints weight = 22980.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.055911 restraints weight = 16022.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.056630 restraints weight = 12532.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.057140 restraints weight = 10663.026| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9955 Z= 0.087 Angle : 0.489 8.969 13565 Z= 0.241 Chirality : 0.040 0.139 1467 Planarity : 0.003 0.028 1745 Dihedral : 3.295 15.969 1409 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.88 % Favored : 97.04 % Rotamer: Outliers : 0.57 % Allowed : 9.20 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.25), residues: 1218 helix: 1.95 (0.26), residues: 411 sheet: 1.03 (0.33), residues: 247 loop : 0.09 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 192 TYR 0.008 0.001 TYR A 158 PHE 0.009 0.001 PHE L 144 TRP 0.009 0.001 TRP A 168 HIS 0.006 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.09 ( 9938) covalent geometry : angle 0.48822 / 0.24 (13529) SS BOND : bond 0.00132 / 0.09 ( 11) SS BOND : angle 0.32376 / 0.17 ( 24) hydrogen bonds : bond 0.02847 / 1.95 ( 417) hydrogen bonds : angle 3.89931 / 2.74 ( 1176) metal coordination : bond 0.00031 / 0.01 ( 2) link_NAG-ASN : bond 0.00198 / 0.09 ( 4) link_NAG-ASN : angle 1.07374 / 0.66 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1713.58 seconds wall clock time: 30 minutes 29.94 seconds (1829.94 seconds total)