Starting phenix.real_space_refine on Mon Jun 9 00:39:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qtj_14142/06_2025/7qtj_14142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qtj_14142/06_2025/7qtj_14142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qtj_14142/06_2025/7qtj_14142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qtj_14142/06_2025/7qtj_14142.map" model { file = "/net/cci-nas-00/data/ceres_data/7qtj_14142/06_2025/7qtj_14142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qtj_14142/06_2025/7qtj_14142.cif" } resolution = 4.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 6285 2.51 5 N 1673 2.21 5 O 1942 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9942 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "C" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "E" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1645 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1637 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.66, per 1000 atoms: 0.67 Number of scatterers: 9942 At special positions: 0 Unit cell: (82.998, 161.846, 152.163, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1942 8.00 N 1673 7.00 C 6285 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 106 " distance=2.03 Simple disulfide: pdb=" SG CYS F 150 " - pdb=" SG CYS F 206 " 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 331 " Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2366 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 26 sheets defined 9.8% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.656A pdb=" N ASP B 31 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.043A pdb=" N THR B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.741A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 removed outlier: 3.529A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 removed outlier: 4.083A pdb=" N GLU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 183 through 187' Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.414A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.838A pdb=" N VAL A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'D' and resid 365 through 371 removed outlier: 3.897A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 3.677A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.196A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 410 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.900A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.783A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.571A pdb=" N LEU B 18 " --> pdb=" O MET B 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.666A pdb=" N LEU B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 50 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY B 59 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.550A pdb=" N LYS B 98 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 132 through 136 removed outlier: 3.567A pdb=" N PHE B 134 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 153 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY B 151 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 156 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR B 188 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 143 through 144 removed outlier: 3.526A pdb=" N ASP B 156 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N TYR B 188 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 166 removed outlier: 3.624A pdb=" N SER B 165 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS B 208 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.898A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.325A pdb=" N LEU C 11 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 114 through 118 removed outlier: 3.844A pdb=" N VAL C 133 " --> pdb=" O PHE C 118 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.171A pdb=" N TRP C 148 " --> pdb=" O GLN C 155 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR C 192 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS C 194 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS C 207 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL C 196 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 205 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.913A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.524A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 356 through 358 removed outlier: 3.776A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR D 396 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 514 " --> pdb=" O TYR D 396 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AB7, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.793A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'E' and resid 46 through 49 removed outlier: 6.282A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 115 through 119 removed outlier: 4.386A pdb=" N SER E 175 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR E 165 " --> pdb=" O SER E 175 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 154 through 156 removed outlier: 4.449A pdb=" N TRP E 149 " --> pdb=" O GLN E 156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.182A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AC6, first strand: chain 'F' and resid 130 through 134 removed outlier: 6.188A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 130 through 134 removed outlier: 6.188A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 161 through 164 334 hydrogen bonds defined for protein. 822 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: 3.29 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2750 1.33 - 1.45: 1966 1.45 - 1.58: 5425 1.58 - 1.70: 1 1.70 - 1.82: 47 Bond restraints: 10189 Sorted by residual: bond pdb=" CG PRO E 121 " pdb=" CD PRO E 121 " ideal model delta sigma weight residual 1.503 1.299 0.204 3.40e-02 8.65e+02 3.59e+01 bond pdb=" CA SER B 52 " pdb=" CB SER B 52 " ideal model delta sigma weight residual 1.531 1.464 0.066 1.48e-02 4.57e+03 2.00e+01 bond pdb=" N PRO E 121 " pdb=" CD PRO E 121 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.09e+01 bond pdb=" CB PRO E 121 " pdb=" CG PRO E 121 " ideal model delta sigma weight residual 1.492 1.645 -0.153 5.00e-02 4.00e+02 9.37e+00 bond pdb=" CA SER B 55 " pdb=" CB SER B 55 " ideal model delta sigma weight residual 1.532 1.488 0.044 1.48e-02 4.57e+03 8.97e+00 ... (remaining 10184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 13784 3.92 - 7.83: 66 7.83 - 11.75: 3 11.75 - 15.67: 3 15.67 - 19.59: 1 Bond angle restraints: 13857 Sorted by residual: angle pdb=" CA PRO E 121 " pdb=" N PRO E 121 " pdb=" CD PRO E 121 " ideal model delta sigma weight residual 112.00 96.57 15.43 1.40e+00 5.10e-01 1.22e+02 angle pdb=" CG ARG A 346 " pdb=" CD ARG A 346 " pdb=" NE ARG A 346 " ideal model delta sigma weight residual 112.00 92.41 19.59 2.20e+00 2.07e-01 7.93e+01 angle pdb=" N PRO E 121 " pdb=" CD PRO E 121 " pdb=" CG PRO E 121 " ideal model delta sigma weight residual 103.20 90.73 12.47 1.50e+00 4.44e-01 6.91e+01 angle pdb=" C PHE A 377 " pdb=" CA PHE A 377 " pdb=" CB PHE A 377 " ideal model delta sigma weight residual 111.85 99.84 12.01 1.47e+00 4.63e-01 6.68e+01 angle pdb=" C THR C 172 " pdb=" CA THR C 172 " pdb=" CB THR C 172 " ideal model delta sigma weight residual 114.40 106.53 7.87 1.25e+00 6.40e-01 3.97e+01 ... (remaining 13852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 5676 21.98 - 43.95: 381 43.95 - 65.93: 51 65.93 - 87.90: 22 87.90 - 109.88: 9 Dihedral angle restraints: 6139 sinusoidal: 2431 harmonic: 3708 Sorted by residual: dihedral pdb=" CB CYS B 152 " pdb=" SG CYS B 152 " pdb=" SG CYS B 208 " pdb=" CB CYS B 208 " ideal model delta sinusoidal sigma weight residual 93.00 159.95 -66.95 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" C PHE A 377 " pdb=" N PHE A 377 " pdb=" CA PHE A 377 " pdb=" CB PHE A 377 " ideal model delta harmonic sigma weight residual -122.60 -107.54 -15.06 0 2.50e+00 1.60e-01 3.63e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -131.63 45.63 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 6136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1416 0.091 - 0.181: 110 0.181 - 0.272: 9 0.272 - 0.362: 3 0.362 - 0.453: 2 Chirality restraints: 1540 Sorted by residual: chirality pdb=" CA PHE A 377 " pdb=" N PHE A 377 " pdb=" C PHE A 377 " pdb=" CB PHE A 377 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" CA ARG A 346 " pdb=" N ARG A 346 " pdb=" C ARG A 346 " pdb=" CB ARG A 346 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA ARG B 72 " pdb=" N ARG B 72 " pdb=" C ARG B 72 " pdb=" CB ARG B 72 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 1537 not shown) Planarity restraints: 1782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 120 " -0.100 5.00e-02 4.00e+02 1.37e-01 2.99e+01 pdb=" N PRO E 121 " 0.236 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 101 " -0.022 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C HIS B 101 " 0.076 2.00e-02 2.50e+03 pdb=" O HIS B 101 " -0.028 2.00e-02 2.50e+03 pdb=" N TYR B 102 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 51 " 0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ILE B 51 " -0.071 2.00e-02 2.50e+03 pdb=" O ILE B 51 " 0.027 2.00e-02 2.50e+03 pdb=" N SER B 52 " 0.024 2.00e-02 2.50e+03 ... (remaining 1779 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 246 2.70 - 3.25: 9271 3.25 - 3.80: 14986 3.80 - 4.35: 19152 4.35 - 4.90: 31923 Nonbonded interactions: 75578 Sorted by model distance: nonbonded pdb=" CB ARG A 346 " pdb=" NE ARG A 346 " model vdw 2.144 2.816 nonbonded pdb=" OE1 GLN C 6 " pdb=" OG1 THR C 102 " model vdw 2.303 3.040 nonbonded pdb=" O PRO B 197 " pdb=" OG SER B 200 " model vdw 2.305 3.040 nonbonded pdb=" NH1 ARG D 403 " pdb=" O GLY D 504 " model vdw 2.310 3.120 nonbonded pdb=" OE2 GLU B 6 " pdb=" N GLY B 118 " model vdw 2.315 3.120 ... (remaining 75573 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.110 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 0.204 10212 Z= 0.211 Angle : 0.748 19.587 13908 Z= 0.425 Chirality : 0.050 0.453 1540 Planarity : 0.005 0.137 1780 Dihedral : 15.202 109.878 3719 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.21 % Favored : 94.48 % Rotamer: Outliers : 1.27 % Allowed : 0.54 % Favored : 98.19 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1268 helix: -2.11 (0.56), residues: 62 sheet: 1.33 (0.25), residues: 440 loop : -0.43 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 148 HIS 0.002 0.001 HIS C 92 PHE 0.029 0.001 PHE A 377 TYR 0.025 0.001 TYR B 102 ARG 0.005 0.000 ARG F 38 Details of bonding type rmsd link_NAG-ASN : bond 0.01025 ( 2) link_NAG-ASN : angle 7.03297 ( 6) link_BETA1-4 : bond 0.00302 ( 3) link_BETA1-4 : angle 3.95648 ( 9) hydrogen bonds : bond 0.17777 ( 297) hydrogen bonds : angle 6.97827 ( 822) SS BOND : bond 0.00271 ( 18) SS BOND : angle 0.62747 ( 36) covalent geometry : bond 0.00410 (10189) covalent geometry : angle 0.72749 (13857) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 167 ASP cc_start: 0.8876 (m-30) cc_final: 0.8606 (m-30) REVERT: A 375 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.6655 (p90) REVERT: D 375 PHE cc_start: 0.5919 (m-10) cc_final: 0.5478 (m-80) REVERT: F 10 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7425 (mm-30) outliers start: 14 outliers final: 4 residues processed: 131 average time/residue: 0.2440 time to fit residues: 43.9987 Evaluate side-chains 85 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 7.9990 chunk 95 optimal weight: 0.1980 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.0020 chunk 73 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN C 6 GLN C 138 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN E 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.120011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.099569 restraints weight = 35249.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.099406 restraints weight = 29552.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.100011 restraints weight = 24415.660| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10212 Z= 0.112 Angle : 0.625 14.501 13908 Z= 0.309 Chirality : 0.045 0.305 1540 Planarity : 0.004 0.050 1780 Dihedral : 8.260 79.048 1497 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.11 % Rotamer: Outliers : 0.27 % Allowed : 5.26 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.24), residues: 1268 helix: -2.21 (0.55), residues: 60 sheet: 1.30 (0.25), residues: 458 loop : -0.42 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 53 HIS 0.003 0.001 HIS B 101 PHE 0.017 0.001 PHE D 429 TYR 0.014 0.001 TYR B 102 ARG 0.004 0.000 ARG F 38 Details of bonding type rmsd link_NAG-ASN : bond 0.01161 ( 2) link_NAG-ASN : angle 6.64286 ( 6) link_BETA1-4 : bond 0.00914 ( 3) link_BETA1-4 : angle 3.42865 ( 9) hydrogen bonds : bond 0.03396 ( 297) hydrogen bonds : angle 5.55963 ( 822) SS BOND : bond 0.00556 ( 18) SS BOND : angle 2.03361 ( 36) covalent geometry : bond 0.00245 (10189) covalent geometry : angle 0.59546 (13857) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8494 (p0) cc_final: 0.8205 (p0) REVERT: A 389 ASP cc_start: 0.9216 (p0) cc_final: 0.8568 (p0) REVERT: A 392 PHE cc_start: 0.8024 (m-80) cc_final: 0.7750 (m-80) REVERT: D 375 PHE cc_start: 0.5751 (m-10) cc_final: 0.5510 (m-80) outliers start: 3 outliers final: 0 residues processed: 125 average time/residue: 0.2249 time to fit residues: 39.6730 Evaluate side-chains 85 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 51 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 44 optimal weight: 0.4980 chunk 67 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.115107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.095682 restraints weight = 36062.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.096065 restraints weight = 40149.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.096335 restraints weight = 41066.477| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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 : 0.005 0.035 10212 Z= 0.205 Angle : 0.697 14.302 13908 Z= 0.351 Chirality : 0.046 0.274 1540 Planarity : 0.004 0.042 1780 Dihedral : 7.047 59.610 1497 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.44 % Favored : 94.32 % Rotamer: Outliers : 0.27 % Allowed : 4.72 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1268 helix: -2.19 (0.59), residues: 54 sheet: 0.76 (0.24), residues: 478 loop : -0.55 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 436 HIS 0.005 0.001 HIS E 199 PHE 0.019 0.002 PHE F 29 TYR 0.017 0.002 TYR B 102 ARG 0.008 0.001 ARG A 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00896 ( 2) link_NAG-ASN : angle 6.81262 ( 6) link_BETA1-4 : bond 0.00890 ( 3) link_BETA1-4 : angle 3.59071 ( 9) hydrogen bonds : bond 0.03747 ( 297) hydrogen bonds : angle 5.59584 ( 822) SS BOND : bond 0.01066 ( 18) SS BOND : angle 2.12073 ( 36) covalent geometry : bond 0.00457 (10189) covalent geometry : angle 0.66883 (13857) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8619 (p0) cc_final: 0.8336 (p0) REVERT: B 99 ASP cc_start: 0.8900 (t0) cc_final: 0.8507 (t0) REVERT: C 194 CYS cc_start: -0.0054 (p) cc_final: -0.0820 (p) REVERT: A 389 ASP cc_start: 0.9289 (p0) cc_final: 0.8755 (p0) REVERT: A 392 PHE cc_start: 0.8206 (m-80) cc_final: 0.7884 (m-80) REVERT: A 406 GLU cc_start: 0.8898 (mp0) cc_final: 0.8637 (mm-30) outliers start: 3 outliers final: 2 residues processed: 117 average time/residue: 0.2529 time to fit residues: 40.8771 Evaluate side-chains 76 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 23 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 117 optimal weight: 0.0070 chunk 3 optimal weight: 0.7980 overall best weight: 1.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.117187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.099064 restraints weight = 35693.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.099709 restraints weight = 42668.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.100266 restraints weight = 34581.110| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10212 Z= 0.134 Angle : 0.641 14.125 13908 Z= 0.319 Chirality : 0.046 0.283 1540 Planarity : 0.004 0.036 1780 Dihedral : 6.344 56.971 1497 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.13 % Favored : 94.64 % Rotamer: Outliers : 0.09 % Allowed : 4.17 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.24), residues: 1268 helix: -2.27 (0.57), residues: 60 sheet: 0.77 (0.24), residues: 471 loop : -0.60 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 436 HIS 0.002 0.001 HIS B 101 PHE 0.031 0.002 PHE C 71 TYR 0.015 0.001 TYR B 102 ARG 0.004 0.000 ARG D 493 Details of bonding type rmsd link_NAG-ASN : bond 0.01056 ( 2) link_NAG-ASN : angle 6.67102 ( 6) link_BETA1-4 : bond 0.01027 ( 3) link_BETA1-4 : angle 3.42824 ( 9) hydrogen bonds : bond 0.03177 ( 297) hydrogen bonds : angle 5.42836 ( 822) SS BOND : bond 0.00913 ( 18) SS BOND : angle 2.08622 ( 36) covalent geometry : bond 0.00300 (10189) covalent geometry : angle 0.61179 (13857) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8512 (p0) cc_final: 0.8247 (p0) REVERT: B 99 ASP cc_start: 0.8625 (t0) cc_final: 0.8267 (t0) REVERT: C 194 CYS cc_start: -0.0163 (p) cc_final: -0.0992 (p) REVERT: A 389 ASP cc_start: 0.9182 (p0) cc_final: 0.8591 (p0) REVERT: A 392 PHE cc_start: 0.8026 (m-80) cc_final: 0.7741 (m-80) outliers start: 1 outliers final: 1 residues processed: 127 average time/residue: 0.2325 time to fit residues: 41.2410 Evaluate side-chains 82 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 2 optimal weight: 7.9990 chunk 48 optimal weight: 0.0570 chunk 13 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 32 optimal weight: 0.2980 chunk 92 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 51 optimal weight: 0.0570 chunk 50 optimal weight: 0.0670 chunk 62 optimal weight: 7.9990 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.119191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.099829 restraints weight = 35244.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.099715 restraints weight = 36770.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.100351 restraints weight = 35878.646| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10212 Z= 0.099 Angle : 0.620 13.801 13908 Z= 0.304 Chirality : 0.045 0.260 1540 Planarity : 0.004 0.034 1780 Dihedral : 5.823 59.122 1497 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.57 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1268 helix: -2.14 (0.61), residues: 55 sheet: 0.87 (0.24), residues: 483 loop : -0.50 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 436 HIS 0.002 0.001 HIS B 101 PHE 0.023 0.001 PHE C 71 TYR 0.013 0.001 TYR B 102 ARG 0.003 0.000 ARG C 108 Details of bonding type rmsd link_NAG-ASN : bond 0.01216 ( 2) link_NAG-ASN : angle 6.44126 ( 6) link_BETA1-4 : bond 0.00885 ( 3) link_BETA1-4 : angle 3.23878 ( 9) hydrogen bonds : bond 0.02751 ( 297) hydrogen bonds : angle 5.16652 ( 822) SS BOND : bond 0.00725 ( 18) SS BOND : angle 1.93374 ( 36) covalent geometry : bond 0.00211 (10189) covalent geometry : angle 0.59277 (13857) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8572 (p0) cc_final: 0.8300 (p0) REVERT: B 99 ASP cc_start: 0.8648 (t0) cc_final: 0.8205 (t0) REVERT: C 70 GLU cc_start: 0.8440 (tt0) cc_final: 0.8194 (tm-30) REVERT: C 140 TYR cc_start: 0.6931 (t80) cc_final: 0.6533 (t80) REVERT: C 145 LYS cc_start: 0.8524 (tppt) cc_final: 0.8297 (tppt) REVERT: C 194 CYS cc_start: -0.0405 (p) cc_final: -0.0939 (p) REVERT: A 389 ASP cc_start: 0.9270 (p0) cc_final: 0.8690 (p0) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2722 time to fit residues: 46.4759 Evaluate side-chains 84 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS D 409 GLN E 91 GLN F 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.111893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.092299 restraints weight = 35848.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.093461 restraints weight = 37421.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.093817 restraints weight = 31129.142| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 10212 Z= 0.295 Angle : 0.799 14.990 13908 Z= 0.409 Chirality : 0.049 0.321 1540 Planarity : 0.005 0.046 1780 Dihedral : 6.444 59.673 1497 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.02 % Favored : 92.74 % Rotamer: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1268 helix: -2.45 (0.58), residues: 61 sheet: 0.37 (0.24), residues: 480 loop : -0.83 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 47 HIS 0.010 0.002 HIS E 199 PHE 0.023 0.002 PHE B 158 TYR 0.026 0.003 TYR C 94 ARG 0.007 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00866 ( 2) link_NAG-ASN : angle 6.94791 ( 6) link_BETA1-4 : bond 0.00791 ( 3) link_BETA1-4 : angle 3.95458 ( 9) hydrogen bonds : bond 0.04290 ( 297) hydrogen bonds : angle 5.89234 ( 822) SS BOND : bond 0.00818 ( 18) SS BOND : angle 2.57248 ( 36) covalent geometry : bond 0.00663 (10189) covalent geometry : angle 0.76993 (13857) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8811 (t0) cc_final: 0.8390 (t0) REVERT: C 14 SER cc_start: 0.9024 (t) cc_final: 0.8787 (m) REVERT: C 140 TYR cc_start: 0.7088 (t80) cc_final: 0.6670 (t80) REVERT: C 194 CYS cc_start: 0.0299 (p) cc_final: -0.0520 (p) REVERT: A 389 ASP cc_start: 0.9257 (p0) cc_final: 0.8808 (p0) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.2642 time to fit residues: 36.1253 Evaluate side-chains 74 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 52 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.116522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.096726 restraints weight = 36161.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.097266 restraints weight = 37049.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.097421 restraints weight = 37730.818| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10212 Z= 0.109 Angle : 0.647 14.190 13908 Z= 0.322 Chirality : 0.045 0.237 1540 Planarity : 0.004 0.036 1780 Dihedral : 5.819 56.911 1497 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.81 % Favored : 94.95 % Rotamer: Outliers : 0.09 % Allowed : 1.45 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.24), residues: 1268 helix: -2.49 (0.56), residues: 61 sheet: 0.55 (0.24), residues: 469 loop : -0.64 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.003 0.001 HIS C 92 PHE 0.017 0.001 PHE D 429 TYR 0.015 0.001 TYR C 94 ARG 0.012 0.001 ARG B 222 Details of bonding type rmsd link_NAG-ASN : bond 0.01213 ( 2) link_NAG-ASN : angle 6.62061 ( 6) link_BETA1-4 : bond 0.00852 ( 3) link_BETA1-4 : angle 3.52304 ( 9) hydrogen bonds : bond 0.03048 ( 297) hydrogen bonds : angle 5.36127 ( 822) SS BOND : bond 0.00576 ( 18) SS BOND : angle 1.86250 ( 36) covalent geometry : bond 0.00237 (10189) covalent geometry : angle 0.62025 (13857) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ASP cc_start: 0.8622 (p0) cc_final: 0.8401 (p0) REVERT: B 99 ASP cc_start: 0.8694 (t0) cc_final: 0.8301 (t0) REVERT: C 14 SER cc_start: 0.8869 (t) cc_final: 0.8666 (m) REVERT: C 140 TYR cc_start: 0.6801 (t80) cc_final: 0.6317 (t80) REVERT: C 145 LYS cc_start: 0.8650 (tppt) cc_final: 0.8431 (tppt) REVERT: C 194 CYS cc_start: -0.0449 (p) cc_final: -0.0973 (p) REVERT: A 389 ASP cc_start: 0.9287 (p0) cc_final: 0.8783 (p0) REVERT: D 454 ARG cc_start: 0.8191 (tpp80) cc_final: 0.7953 (mmm-85) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.2658 time to fit residues: 44.7011 Evaluate side-chains 87 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 84 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.113164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.093928 restraints weight = 36130.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.093876 restraints weight = 41841.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.094340 restraints weight = 42996.012| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10212 Z= 0.217 Angle : 0.738 14.709 13908 Z= 0.372 Chirality : 0.047 0.297 1540 Planarity : 0.005 0.050 1780 Dihedral : 6.116 57.767 1497 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.10 % Favored : 92.67 % Rotamer: Outliers : 0.09 % Allowed : 1.27 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.24), residues: 1268 helix: -2.71 (0.52), residues: 67 sheet: 0.39 (0.24), residues: 473 loop : -0.88 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 50 HIS 0.006 0.002 HIS E 199 PHE 0.018 0.002 PHE B 158 TYR 0.020 0.002 TYR E 33 ARG 0.005 0.001 ARG B 38 Details of bonding type rmsd link_NAG-ASN : bond 0.01012 ( 2) link_NAG-ASN : angle 6.82273 ( 6) link_BETA1-4 : bond 0.00722 ( 3) link_BETA1-4 : angle 3.81003 ( 9) hydrogen bonds : bond 0.03675 ( 297) hydrogen bonds : angle 5.63374 ( 822) SS BOND : bond 0.00679 ( 18) SS BOND : angle 2.63469 ( 36) covalent geometry : bond 0.00492 (10189) covalent geometry : angle 0.70642 (13857) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8824 (t0) cc_final: 0.8396 (t0) REVERT: C 14 SER cc_start: 0.9005 (t) cc_final: 0.8787 (m) REVERT: C 82 ASP cc_start: 0.8594 (m-30) cc_final: 0.8252 (m-30) REVERT: C 140 TYR cc_start: 0.7078 (t80) cc_final: 0.6489 (t80) REVERT: C 194 CYS cc_start: -0.0241 (p) cc_final: -0.0767 (p) REVERT: A 389 ASP cc_start: 0.9203 (p0) cc_final: 0.8755 (p0) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.2888 time to fit residues: 43.4975 Evaluate side-chains 83 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 123 optimal weight: 0.7980 chunk 14 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 88 optimal weight: 0.0070 overall best weight: 3.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.112024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.092746 restraints weight = 35920.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.093267 restraints weight = 40570.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.093613 restraints weight = 39091.318| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10212 Z= 0.229 Angle : 0.749 14.926 13908 Z= 0.380 Chirality : 0.047 0.273 1540 Planarity : 0.005 0.041 1780 Dihedral : 6.301 57.561 1497 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.02 % Favored : 92.74 % Rotamer: Outliers : 0.09 % Allowed : 1.36 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.24), residues: 1268 helix: -2.76 (0.52), residues: 67 sheet: 0.15 (0.24), residues: 477 loop : -1.04 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 50 HIS 0.005 0.001 HIS E 199 PHE 0.042 0.002 PHE C 71 TYR 0.028 0.002 TYR F 155 ARG 0.005 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.01032 ( 2) link_NAG-ASN : angle 6.95609 ( 6) link_BETA1-4 : bond 0.00807 ( 3) link_BETA1-4 : angle 3.88800 ( 9) hydrogen bonds : bond 0.03835 ( 297) hydrogen bonds : angle 5.89567 ( 822) SS BOND : bond 0.00752 ( 18) SS BOND : angle 2.48134 ( 36) covalent geometry : bond 0.00520 (10189) covalent geometry : angle 0.71827 (13857) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8839 (t0) cc_final: 0.8439 (t0) REVERT: C 14 SER cc_start: 0.9067 (t) cc_final: 0.8853 (m) REVERT: C 70 GLU cc_start: 0.8607 (tt0) cc_final: 0.8320 (tm-30) REVERT: C 82 ASP cc_start: 0.8885 (m-30) cc_final: 0.8317 (m-30) REVERT: C 94 TYR cc_start: 0.8135 (t80) cc_final: 0.7706 (t80) REVERT: C 140 TYR cc_start: 0.7176 (t80) cc_final: 0.6547 (t80) REVERT: C 145 LYS cc_start: 0.8479 (tppt) cc_final: 0.8237 (tppt) REVERT: C 194 CYS cc_start: -0.0193 (p) cc_final: -0.0660 (p) REVERT: A 389 ASP cc_start: 0.9291 (p0) cc_final: 0.8844 (p0) REVERT: A 414 GLN cc_start: 0.7111 (tm-30) cc_final: 0.6901 (tm-30) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.2751 time to fit residues: 40.3851 Evaluate side-chains 82 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 2 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 118 optimal weight: 40.0000 chunk 69 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 109 optimal weight: 0.1980 chunk 71 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN F 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.114688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.094729 restraints weight = 35602.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.094732 restraints weight = 35037.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.095089 restraints weight = 36393.966| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10212 Z= 0.120 Angle : 0.672 14.653 13908 Z= 0.334 Chirality : 0.045 0.230 1540 Planarity : 0.004 0.038 1780 Dihedral : 5.894 59.335 1497 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.60 % Favored : 94.16 % Rotamer: Outliers : 0.09 % Allowed : 0.36 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.24), residues: 1268 helix: -2.64 (0.52), residues: 67 sheet: 0.27 (0.24), residues: 470 loop : -0.88 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 50 HIS 0.002 0.001 HIS B 101 PHE 0.029 0.002 PHE D 392 TYR 0.012 0.001 TYR C 140 ARG 0.005 0.000 ARG F 67 Details of bonding type rmsd link_NAG-ASN : bond 0.01146 ( 2) link_NAG-ASN : angle 6.83410 ( 6) link_BETA1-4 : bond 0.00801 ( 3) link_BETA1-4 : angle 3.73235 ( 9) hydrogen bonds : bond 0.03112 ( 297) hydrogen bonds : angle 5.55047 ( 822) SS BOND : bond 0.00519 ( 18) SS BOND : angle 2.17458 ( 36) covalent geometry : bond 0.00268 (10189) covalent geometry : angle 0.64171 (13857) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 99 ASP cc_start: 0.8721 (t0) cc_final: 0.8321 (t0) REVERT: C 14 SER cc_start: 0.8862 (t) cc_final: 0.8650 (m) REVERT: C 70 GLU cc_start: 0.8566 (tt0) cc_final: 0.8266 (tm-30) REVERT: C 82 ASP cc_start: 0.8783 (m-30) cc_final: 0.8360 (m-30) REVERT: C 94 TYR cc_start: 0.7887 (t80) cc_final: 0.7556 (t80) REVERT: C 140 TYR cc_start: 0.7128 (t80) cc_final: 0.6591 (t80) REVERT: C 194 CYS cc_start: -0.0303 (p) cc_final: -0.0875 (p) REVERT: A 389 ASP cc_start: 0.9175 (p0) cc_final: 0.8699 (p0) REVERT: D 375 PHE cc_start: 0.5142 (m-80) cc_final: 0.4902 (m-80) REVERT: D 454 ARG cc_start: 0.8329 (tpp80) cc_final: 0.8014 (mmm-85) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.2467 time to fit residues: 38.8846 Evaluate side-chains 80 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 4 optimal weight: 0.0470 chunk 56 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 7 optimal weight: 0.0170 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.116212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.096496 restraints weight = 35613.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.097310 restraints weight = 33709.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.097789 restraints weight = 29371.343| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10212 Z= 0.108 Angle : 0.654 14.375 13908 Z= 0.325 Chirality : 0.045 0.187 1540 Planarity : 0.004 0.036 1780 Dihedral : 5.481 54.512 1497 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.89 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1268 helix: -2.68 (0.51), residues: 67 sheet: 0.38 (0.24), residues: 472 loop : -0.76 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 50 HIS 0.002 0.000 HIS B 212 PHE 0.024 0.001 PHE C 71 TYR 0.021 0.001 TYR D 351 ARG 0.006 0.000 ARG F 67 Details of bonding type rmsd link_NAG-ASN : bond 0.01137 ( 2) link_NAG-ASN : angle 6.67646 ( 6) link_BETA1-4 : bond 0.00836 ( 3) link_BETA1-4 : angle 3.59879 ( 9) hydrogen bonds : bond 0.03030 ( 297) hydrogen bonds : angle 5.34960 ( 822) SS BOND : bond 0.00445 ( 18) SS BOND : angle 1.73534 ( 36) covalent geometry : bond 0.00241 (10189) covalent geometry : angle 0.62737 (13857) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3261.92 seconds wall clock time: 58 minutes 38.82 seconds (3518.82 seconds total)