Starting phenix.real_space_refine on Thu Jun 12 20:55:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pm4_13520/06_2025/7pm4_13520.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm4_13520/06_2025/7pm4_13520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pm4_13520/06_2025/7pm4_13520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm4_13520/06_2025/7pm4_13520.map" model { file = "/net/cci-nas-00/data/ceres_data/7pm4_13520/06_2025/7pm4_13520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm4_13520/06_2025/7pm4_13520.cif" } resolution = 2.49 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= 0.002 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 40 5.16 5 C 9276 2.51 5 N 2340 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14288 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3533 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'DFU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Restraints were copied for chains: C, B, D Time building chain proxies: 8.67, per 1000 atoms: 0.61 Number of scatterers: 14288 At special positions: 0 Unit cell: (159.408, 113.488, 59.696, 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 40 16.00 O 2632 8.00 N 2340 7.00 C 9276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS D 266 " - pdb=" SG CYS D 274 " 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 501 " - " ASN A 236 " " NAG B 501 " - " ASN B 236 " " NAG C 501 " - " ASN C 236 " " NAG D 501 " - " ASN D 236 " Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 36.0% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 45 through 52 removed outlier: 4.197A pdb=" N ASP A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 81 through 92 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 100 through 105 removed outlier: 4.476A pdb=" N GLN A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 343 through 361 removed outlier: 3.668A pdb=" N ILE A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 45 through 52 removed outlier: 4.197A pdb=" N ASP B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 71 through 77 Processing helix chain 'B' and resid 81 through 92 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 100 through 105 removed outlier: 4.476A pdb=" N GLN B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'B' and resid 343 through 361 removed outlier: 3.668A pdb=" N ILE B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 45 through 52 removed outlier: 4.197A pdb=" N ASP C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 81 through 92 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 100 through 105 removed outlier: 4.476A pdb=" N GLN C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 185 through 194 Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 236 through 247 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'C' and resid 343 through 361 removed outlier: 3.668A pdb=" N ILE C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'D' and resid 35 through 40 Processing helix chain 'D' and resid 45 through 52 removed outlier: 4.197A pdb=" N ASP D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 71 through 77 Processing helix chain 'D' and resid 81 through 92 Processing helix chain 'D' and resid 97 through 99 No H-bonds generated for 'chain 'D' and resid 97 through 99' Processing helix chain 'D' and resid 100 through 105 removed outlier: 4.476A pdb=" N GLN D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 185 through 194 Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 236 through 247 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'D' and resid 343 through 361 removed outlier: 3.668A pdb=" N ILE D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 256 removed outlier: 6.314A pdb=" N VAL A 127 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR A 177 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 129 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N SER A 179 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR A 131 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 126 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 368 through 374 removed outlier: 4.258A pdb=" N TRP A 370 " --> pdb=" O TYR A 383 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N TYR A 383 " --> pdb=" O TRP A 370 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N VAL A 372 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL A 381 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL A 460 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR A 413 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS A 426 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 256 removed outlier: 6.314A pdb=" N VAL B 127 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR B 177 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 129 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N SER B 179 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR B 131 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 126 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 368 through 374 removed outlier: 4.258A pdb=" N TRP B 370 " --> pdb=" O TYR B 383 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N TYR B 383 " --> pdb=" O TRP B 370 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N VAL B 372 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL B 381 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 460 " --> pdb=" O THR B 413 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR B 413 " --> pdb=" O VAL B 460 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS B 426 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 255 through 256 removed outlier: 6.314A pdb=" N VAL C 127 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR C 177 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 129 " --> pdb=" O TYR C 177 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N SER C 179 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR C 131 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 126 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 368 through 374 removed outlier: 4.258A pdb=" N TRP C 370 " --> pdb=" O TYR C 383 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N TYR C 383 " --> pdb=" O TRP C 370 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N VAL C 372 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL C 381 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL C 460 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR C 413 " --> pdb=" O VAL C 460 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS C 426 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 255 through 256 removed outlier: 6.314A pdb=" N VAL D 127 " --> pdb=" O GLY D 175 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR D 177 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU D 129 " --> pdb=" O TYR D 177 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N SER D 179 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR D 131 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 126 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 368 through 374 removed outlier: 4.258A pdb=" N TRP D 370 " --> pdb=" O TYR D 383 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N TYR D 383 " --> pdb=" O TRP D 370 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N VAL D 372 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N VAL D 381 " --> pdb=" O VAL D 372 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL D 460 " --> pdb=" O THR D 413 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR D 413 " --> pdb=" O VAL D 460 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS D 426 " --> pdb=" O SER D 438 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1440 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: 4.11 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4368 1.34 - 1.46: 4052 1.46 - 1.58: 6300 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 14780 Sorted by residual: bond pdb=" C1 DFU A 502 " pdb=" N5 DFU A 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C1 DFU D 502 " pdb=" N5 DFU D 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C1 DFU B 502 " pdb=" N5 DFU B 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C1 DFU C 502 " pdb=" N5 DFU C 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C5 DFU D 502 " pdb=" N5 DFU D 502 " ideal model delta sigma weight residual 1.465 1.500 -0.035 2.00e-02 2.50e+03 3.10e+00 ... (remaining 14775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 19740 1.38 - 2.77: 332 2.77 - 4.15: 100 4.15 - 5.54: 32 5.54 - 6.92: 16 Bond angle restraints: 20220 Sorted by residual: angle pdb=" C THR D 410 " pdb=" N THR D 411 " pdb=" CA THR D 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C THR B 410 " pdb=" N THR B 411 " pdb=" CA THR B 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C THR C 410 " pdb=" N THR C 411 " pdb=" CA THR C 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C THR A 410 " pdb=" N THR A 411 " pdb=" CA THR A 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" CG LYS D 426 " pdb=" CD LYS D 426 " pdb=" CE LYS D 426 " ideal model delta sigma weight residual 111.30 117.30 -6.00 2.30e+00 1.89e-01 6.80e+00 ... (remaining 20215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 7388 17.61 - 35.21: 748 35.21 - 52.82: 228 52.82 - 70.42: 76 70.42 - 88.03: 24 Dihedral angle restraints: 8464 sinusoidal: 3468 harmonic: 4996 Sorted by residual: dihedral pdb=" CB CYS D 266 " pdb=" SG CYS D 266 " pdb=" SG CYS D 274 " pdb=" CB CYS D 274 " ideal model delta sinusoidal sigma weight residual 93.00 161.31 -68.31 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS C 266 " pdb=" SG CYS C 266 " pdb=" SG CYS C 274 " pdb=" CB CYS C 274 " ideal model delta sinusoidal sigma weight residual 93.00 161.31 -68.31 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS B 266 " pdb=" SG CYS B 266 " pdb=" SG CYS B 274 " pdb=" CB CYS B 274 " ideal model delta sinusoidal sigma weight residual 93.00 161.31 -68.31 1 1.00e+01 1.00e-02 6.05e+01 ... (remaining 8461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1172 0.029 - 0.058: 540 0.058 - 0.087: 196 0.087 - 0.115: 124 0.115 - 0.144: 20 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA ILE C 455 " pdb=" N ILE C 455 " pdb=" C ILE C 455 " pdb=" CB ILE C 455 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE B 455 " pdb=" N ILE B 455 " pdb=" C ILE B 455 " pdb=" CB ILE B 455 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE A 455 " pdb=" N ILE A 455 " pdb=" C ILE A 455 " pdb=" CB ILE A 455 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 2049 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 418 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C MET A 418 " 0.031 2.00e-02 2.50e+03 pdb=" O MET A 418 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 419 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 418 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C MET C 418 " -0.031 2.00e-02 2.50e+03 pdb=" O MET C 418 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU C 419 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 418 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C MET B 418 " 0.031 2.00e-02 2.50e+03 pdb=" O MET B 418 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 419 " -0.010 2.00e-02 2.50e+03 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2536 2.77 - 3.30: 13354 3.30 - 3.83: 26460 3.83 - 4.37: 32936 4.37 - 4.90: 52980 Nonbonded interactions: 128266 Sorted by model distance: nonbonded pdb=" OG1 THR C 378 " pdb=" N THR C 379 " model vdw 2.237 3.120 nonbonded pdb=" OG1 THR D 378 " pdb=" N THR D 379 " model vdw 2.237 3.120 nonbonded pdb=" OG1 THR A 378 " pdb=" N THR A 379 " model vdw 2.237 3.120 nonbonded pdb=" OG1 THR B 378 " pdb=" N THR B 379 " model vdw 2.237 3.120 nonbonded pdb=" O SER B 445 " pdb=" OG SER B 445 " model vdw 2.253 3.040 ... (remaining 128261 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.130 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: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.220 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14788 Z= 0.141 Angle : 0.564 6.924 20240 Z= 0.287 Chirality : 0.043 0.144 2052 Planarity : 0.004 0.034 2548 Dihedral : 16.861 88.029 5252 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.06 % Allowed : 16.22 % Favored : 82.71 % 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: 0.76 (0.21), residues: 1716 helix: 1.44 (0.23), residues: 512 sheet: 0.06 (0.29), residues: 284 loop : 0.23 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 223 HIS 0.002 0.000 HIS A 286 PHE 0.010 0.001 PHE A 394 TYR 0.010 0.001 TYR D 177 ARG 0.001 0.000 ARG C 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 4) link_NAG-ASN : angle 2.48175 ( 12) hydrogen bonds : bond 0.12488 ( 508) hydrogen bonds : angle 5.22545 ( 1440) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.86715 ( 8) covalent geometry : bond 0.00300 (14780) covalent geometry : angle 0.56031 (20220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.507 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 1.1958 time to fit residues: 154.1454 Evaluate side-chains 108 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.9980 chunk 130 optimal weight: 0.1980 chunk 72 optimal weight: 0.0270 chunk 44 optimal weight: 0.3980 chunk 87 optimal weight: 0.0980 chunk 69 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.2838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.089013 restraints weight = 15965.745| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.51 r_work: 0.2840 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 14788 Z= 0.092 Angle : 0.495 5.737 20240 Z= 0.255 Chirality : 0.042 0.140 2052 Planarity : 0.004 0.032 2548 Dihedral : 4.543 36.238 2024 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.60 % Allowed : 14.36 % Favored : 84.04 % 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 (0.21), residues: 1716 helix: 1.58 (0.23), residues: 540 sheet: 0.17 (0.29), residues: 284 loop : 0.14 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 183 HIS 0.001 0.000 HIS B 286 PHE 0.008 0.001 PHE C 394 TYR 0.007 0.001 TYR A 92 ARG 0.001 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 4) link_NAG-ASN : angle 1.58929 ( 12) hydrogen bonds : bond 0.03263 ( 508) hydrogen bonds : angle 4.42560 ( 1440) SS BOND : bond 0.00090 ( 4) SS BOND : angle 0.51639 ( 8) covalent geometry : bond 0.00195 (14780) covalent geometry : angle 0.49339 (20220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.640 Fit side-chains REVERT: A 315 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7946 (tp30) REVERT: B 315 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7957 (tp30) REVERT: C 315 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7959 (tp30) REVERT: D 315 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7956 (tp30) outliers start: 24 outliers final: 8 residues processed: 128 average time/residue: 1.1514 time to fit residues: 164.1392 Evaluate side-chains 100 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 68 optimal weight: 0.0980 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.087476 restraints weight = 15953.368| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.50 r_work: 0.2810 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14788 Z= 0.105 Angle : 0.505 5.829 20240 Z= 0.260 Chirality : 0.043 0.139 2052 Planarity : 0.004 0.032 2548 Dihedral : 4.346 33.694 2012 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.86 % Allowed : 13.83 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1716 helix: 1.53 (0.23), residues: 560 sheet: 0.28 (0.29), residues: 284 loop : 0.12 (0.24), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 223 HIS 0.001 0.000 HIS B 178 PHE 0.009 0.001 PHE C 96 TYR 0.009 0.001 TYR C 92 ARG 0.001 0.000 ARG C 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 4) link_NAG-ASN : angle 1.98866 ( 12) hydrogen bonds : bond 0.03633 ( 508) hydrogen bonds : angle 4.46580 ( 1440) SS BOND : bond 0.00196 ( 4) SS BOND : angle 0.60987 ( 8) covalent geometry : bond 0.00230 (14780) covalent geometry : angle 0.50255 (20220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 1.448 Fit side-chains REVERT: A 315 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: B 315 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7994 (tp30) REVERT: C 315 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7998 (tp30) REVERT: D 315 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7992 (tp30) outliers start: 28 outliers final: 12 residues processed: 120 average time/residue: 1.1217 time to fit residues: 150.4361 Evaluate side-chains 112 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 60 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 82 optimal weight: 0.0470 chunk 15 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.087312 restraints weight = 15854.522| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.49 r_work: 0.2810 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14788 Z= 0.106 Angle : 0.506 5.852 20240 Z= 0.260 Chirality : 0.043 0.139 2052 Planarity : 0.004 0.032 2548 Dihedral : 4.318 32.459 2012 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.39 % Allowed : 13.30 % Favored : 84.31 % 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: 0.89 (0.22), residues: 1716 helix: 1.56 (0.23), residues: 560 sheet: 0.34 (0.30), residues: 284 loop : 0.13 (0.24), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 243 HIS 0.001 0.000 HIS C 111 PHE 0.009 0.001 PHE C 394 TYR 0.009 0.001 TYR C 92 ARG 0.001 0.000 ARG B 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 4) link_NAG-ASN : angle 2.02836 ( 12) hydrogen bonds : bond 0.03607 ( 508) hydrogen bonds : angle 4.43750 ( 1440) SS BOND : bond 0.00205 ( 4) SS BOND : angle 0.61238 ( 8) covalent geometry : bond 0.00236 (14780) covalent geometry : angle 0.50381 (20220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 1.488 Fit side-chains REVERT: A 315 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7995 (tp30) REVERT: B 315 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7994 (tp30) REVERT: C 315 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8001 (tp30) REVERT: D 315 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7996 (tp30) outliers start: 36 outliers final: 16 residues processed: 128 average time/residue: 1.0618 time to fit residues: 152.8685 Evaluate side-chains 120 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 106 optimal weight: 2.9990 chunk 135 optimal weight: 0.1980 chunk 129 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 97 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.087451 restraints weight = 15990.750| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.50 r_work: 0.2813 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14788 Z= 0.104 Angle : 0.504 5.851 20240 Z= 0.259 Chirality : 0.043 0.140 2052 Planarity : 0.004 0.033 2548 Dihedral : 4.277 31.137 2012 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.39 % Allowed : 13.56 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1716 helix: 1.53 (0.23), residues: 560 sheet: 0.37 (0.30), residues: 284 loop : 0.16 (0.24), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 243 HIS 0.001 0.000 HIS D 111 PHE 0.009 0.001 PHE B 394 TYR 0.009 0.001 TYR B 92 ARG 0.001 0.000 ARG C 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 4) link_NAG-ASN : angle 1.98750 ( 12) hydrogen bonds : bond 0.03540 ( 508) hydrogen bonds : angle 4.42010 ( 1440) SS BOND : bond 0.00199 ( 4) SS BOND : angle 0.59744 ( 8) covalent geometry : bond 0.00231 (14780) covalent geometry : angle 0.50138 (20220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 1.590 Fit side-chains REVERT: A 315 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8009 (tp30) REVERT: B 315 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8011 (tp30) REVERT: C 315 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8013 (tp30) REVERT: D 315 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8005 (tp30) outliers start: 36 outliers final: 20 residues processed: 124 average time/residue: 1.1492 time to fit residues: 158.9643 Evaluate side-chains 120 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 124 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 156 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 92 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.087522 restraints weight = 16033.629| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.50 r_work: 0.2811 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14788 Z= 0.106 Angle : 0.505 5.859 20240 Z= 0.260 Chirality : 0.043 0.140 2052 Planarity : 0.004 0.032 2548 Dihedral : 4.273 30.376 2012 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.13 % Allowed : 13.83 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1716 helix: 1.52 (0.23), residues: 560 sheet: 0.39 (0.30), residues: 284 loop : 0.16 (0.24), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 243 HIS 0.001 0.000 HIS A 111 PHE 0.009 0.001 PHE C 394 TYR 0.009 0.001 TYR C 92 ARG 0.001 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 4) link_NAG-ASN : angle 2.02667 ( 12) hydrogen bonds : bond 0.03554 ( 508) hydrogen bonds : angle 4.43368 ( 1440) SS BOND : bond 0.00208 ( 4) SS BOND : angle 0.61427 ( 8) covalent geometry : bond 0.00236 (14780) covalent geometry : angle 0.50307 (20220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 1.482 Fit side-chains REVERT: A 315 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8011 (tp30) REVERT: B 315 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8017 (tp30) REVERT: C 315 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8019 (tp30) REVERT: D 315 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8013 (tp30) outliers start: 32 outliers final: 20 residues processed: 124 average time/residue: 1.1469 time to fit residues: 158.4359 Evaluate side-chains 120 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 3 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.087624 restraints weight = 15918.418| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.50 r_work: 0.2814 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14788 Z= 0.106 Angle : 0.506 5.860 20240 Z= 0.260 Chirality : 0.043 0.141 2052 Planarity : 0.004 0.032 2548 Dihedral : 4.262 29.969 2012 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.86 % Allowed : 14.10 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1716 helix: 1.51 (0.23), residues: 560 sheet: 0.40 (0.30), residues: 284 loop : 0.17 (0.24), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 243 HIS 0.001 0.000 HIS B 111 PHE 0.009 0.001 PHE A 394 TYR 0.009 0.001 TYR A 92 ARG 0.001 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 4) link_NAG-ASN : angle 2.00659 ( 12) hydrogen bonds : bond 0.03547 ( 508) hydrogen bonds : angle 4.43001 ( 1440) SS BOND : bond 0.00208 ( 4) SS BOND : angle 0.61467 ( 8) covalent geometry : bond 0.00236 (14780) covalent geometry : angle 0.50357 (20220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 1.780 Fit side-chains REVERT: A 315 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8001 (tp30) REVERT: B 315 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8007 (tp30) REVERT: C 315 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8007 (tp30) REVERT: D 315 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8006 (tp30) outliers start: 28 outliers final: 20 residues processed: 124 average time/residue: 1.5425 time to fit residues: 212.6856 Evaluate side-chains 120 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 0.0570 chunk 152 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.087048 restraints weight = 15762.727| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.49 r_work: 0.2805 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14788 Z= 0.115 Angle : 0.518 5.904 20240 Z= 0.267 Chirality : 0.043 0.142 2052 Planarity : 0.004 0.032 2548 Dihedral : 4.345 30.294 2012 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.86 % Allowed : 14.36 % Favored : 83.78 % 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: 0.87 (0.22), residues: 1716 helix: 1.47 (0.23), residues: 560 sheet: 0.39 (0.30), residues: 284 loop : 0.15 (0.24), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.001 0.001 HIS D 111 PHE 0.009 0.002 PHE B 394 TYR 0.010 0.001 TYR B 92 ARG 0.002 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00298 ( 4) link_NAG-ASN : angle 2.14402 ( 12) hydrogen bonds : bond 0.03713 ( 508) hydrogen bonds : angle 4.50426 ( 1440) SS BOND : bond 0.00233 ( 4) SS BOND : angle 0.66252 ( 8) covalent geometry : bond 0.00259 (14780) covalent geometry : angle 0.51587 (20220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 1.535 Fit side-chains REVERT: A 315 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7987 (tp30) REVERT: B 315 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7992 (tp30) REVERT: C 315 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7994 (tp30) REVERT: D 315 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7991 (tp30) outliers start: 28 outliers final: 20 residues processed: 112 average time/residue: 1.1306 time to fit residues: 141.9853 Evaluate side-chains 120 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 46 optimal weight: 0.3980 chunk 171 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 160 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.087420 restraints weight = 15839.151| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.49 r_work: 0.2809 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14788 Z= 0.110 Angle : 0.514 5.884 20240 Z= 0.264 Chirality : 0.043 0.143 2052 Planarity : 0.004 0.032 2548 Dihedral : 4.303 29.319 2012 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.86 % Allowed : 14.36 % Favored : 83.78 % 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: 0.89 (0.22), residues: 1716 helix: 1.49 (0.23), residues: 560 sheet: 0.41 (0.30), residues: 284 loop : 0.16 (0.24), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 243 HIS 0.001 0.001 HIS A 286 PHE 0.009 0.001 PHE B 394 TYR 0.009 0.001 TYR C 92 ARG 0.002 0.000 ARG A 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 4) link_NAG-ASN : angle 2.06127 ( 12) hydrogen bonds : bond 0.03617 ( 508) hydrogen bonds : angle 4.47486 ( 1440) SS BOND : bond 0.00223 ( 4) SS BOND : angle 0.65146 ( 8) covalent geometry : bond 0.00247 (14780) covalent geometry : angle 0.51130 (20220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 1.490 Fit side-chains REVERT: A 315 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7994 (tp30) REVERT: B 315 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8000 (tp30) REVERT: C 315 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7999 (tp30) REVERT: D 315 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7995 (tp30) outliers start: 28 outliers final: 20 residues processed: 114 average time/residue: 1.2252 time to fit residues: 157.4165 Evaluate side-chains 118 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 0.0770 chunk 53 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 97 optimal weight: 0.0970 chunk 163 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.086479 restraints weight = 15803.850| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.49 r_work: 0.2795 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14788 Z= 0.126 Angle : 0.534 5.970 20240 Z= 0.275 Chirality : 0.044 0.144 2052 Planarity : 0.004 0.032 2548 Dihedral : 4.452 30.181 2012 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.13 % Allowed : 13.83 % Favored : 84.04 % 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: 0.82 (0.22), residues: 1716 helix: 1.43 (0.23), residues: 560 sheet: 0.38 (0.30), residues: 284 loop : 0.12 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 260 HIS 0.002 0.001 HIS B 111 PHE 0.009 0.002 PHE C 394 TYR 0.010 0.001 TYR A 92 ARG 0.002 0.000 ARG C 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00335 ( 4) link_NAG-ASN : angle 2.27746 ( 12) hydrogen bonds : bond 0.03901 ( 508) hydrogen bonds : angle 4.55878 ( 1440) SS BOND : bond 0.00271 ( 4) SS BOND : angle 0.71322 ( 8) covalent geometry : bond 0.00286 (14780) covalent geometry : angle 0.53168 (20220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 1.598 Fit side-chains REVERT: A 315 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7969 (tp30) REVERT: B 315 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: C 315 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7993 (tp30) REVERT: D 315 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7982 (tp30) outliers start: 32 outliers final: 20 residues processed: 120 average time/residue: 1.3298 time to fit residues: 178.1136 Evaluate side-chains 118 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 134 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.087115 restraints weight = 16013.183| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.50 r_work: 0.2803 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14788 Z= 0.116 Angle : 0.531 6.785 20240 Z= 0.271 Chirality : 0.043 0.143 2052 Planarity : 0.004 0.032 2548 Dihedral : 4.380 29.584 2012 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.86 % Allowed : 13.83 % Favored : 84.31 % 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: 0.84 (0.22), residues: 1716 helix: 1.45 (0.23), residues: 560 sheet: 0.39 (0.30), residues: 284 loop : 0.13 (0.24), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 243 HIS 0.001 0.001 HIS A 111 PHE 0.009 0.001 PHE A 394 TYR 0.009 0.001 TYR C 92 ARG 0.002 0.000 ARG D 86 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 4) link_NAG-ASN : angle 2.13738 ( 12) hydrogen bonds : bond 0.03717 ( 508) hydrogen bonds : angle 4.52699 ( 1440) SS BOND : bond 0.00238 ( 4) SS BOND : angle 0.68478 ( 8) covalent geometry : bond 0.00262 (14780) covalent geometry : angle 0.52835 (20220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9816.88 seconds wall clock time: 171 minutes 35.80 seconds (10295.80 seconds total)