Starting phenix.real_space_refine on Thu Sep 26 22:55:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/09_2024/7pm4_13520.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/09_2024/7pm4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/09_2024/7pm4_13520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/09_2024/7pm4_13520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/09_2024/7pm4_13520.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/09_2024/7pm4_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-5461/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: 8.57, per 1000 atoms: 0.60 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 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: 3.20 Conformation dependent library (CDL) restraints added in 2.0 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: 1.70 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: 4.36 Time building geometry restraints manager: 3.85 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: 7385 17.61 - 35.21: 745 35.21 - 52.82: 228 52.82 - 70.42: 73 70.42 - 88.03: 24 Dihedral angle restraints: 8455 sinusoidal: 3459 harmonic: 4996 Sorted by residual: dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 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=" CA ASP B 247 " pdb=" CB ASP B 247 " pdb=" CG ASP B 247 " pdb=" OD1 ASP B 247 " ideal model delta sinusoidal sigma weight residual -30.00 -87.22 57.22 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASP D 247 " pdb=" CB ASP D 247 " pdb=" CG ASP D 247 " pdb=" OD1 ASP D 247 " ideal model delta sinusoidal sigma weight residual -30.00 -87.22 57.22 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 8452 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: 2.03 - 2.61: 127 2.61 - 3.18: 11904 3.18 - 3.75: 24124 3.75 - 4.33: 36044 4.33 - 4.90: 56076 Nonbonded interactions: 128275 Sorted by model distance: nonbonded pdb=" SG CYS D 266 " pdb=" SG CYS D 274 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS B 266 " pdb=" SG CYS B 274 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS C 266 " pdb=" SG CYS C 274 " model vdw 2.033 3.760 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 ... (remaining 128270 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 'B' selection = chain 'C' 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: 5.640 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.190 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.830 ------------------------------------------------------------------------------- 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 14780 Z= 0.194 Angle : 0.560 6.924 20220 Z= 0.287 Chirality : 0.043 0.144 2052 Planarity : 0.004 0.034 2548 Dihedral : 16.861 88.029 5252 Min Nonbonded Distance : 2.033 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 *********************** 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 fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.459 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 1.2144 time to fit residues: 156.2519 Evaluate side-chains 108 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.575 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 14780 Z= 0.126 Angle : 0.495 5.731 20220 Z= 0.256 Chirality : 0.042 0.139 2052 Planarity : 0.004 0.032 2548 Dihedral : 4.610 36.663 2024 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.60 % Allowed : 14.10 % 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 (0.21), residues: 1716 helix: 1.58 (0.23), residues: 540 sheet: 0.17 (0.29), residues: 284 loop : 0.15 (0.23), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 183 HIS 0.001 0.000 HIS B 286 PHE 0.008 0.001 PHE D 394 TYR 0.007 0.001 TYR C 92 ARG 0.001 0.000 ARG C 86 *********************** 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 135 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 1.548 Fit side-chains REVERT: A 315 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7442 (tp30) REVERT: B 315 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7441 (tp30) REVERT: C 315 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7441 (tp30) REVERT: D 315 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7441 (tp30) outliers start: 24 outliers final: 8 residues processed: 131 average time/residue: 1.1107 time to fit residues: 162.3553 Evaluate side-chains 103 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 86 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 169 optimal weight: 0.5980 chunk 139 optimal weight: 0.4980 chunk 155 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14780 Z= 0.225 Angle : 0.554 6.028 20220 Z= 0.289 Chirality : 0.045 0.144 2052 Planarity : 0.005 0.034 2548 Dihedral : 4.763 36.189 2012 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.39 % Allowed : 13.03 % Favored : 84.57 % 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 (0.21), residues: 1716 helix: 1.36 (0.23), residues: 560 sheet: 0.21 (0.30), residues: 284 loop : 0.00 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 223 HIS 0.002 0.001 HIS A 178 PHE 0.011 0.002 PHE A 96 TYR 0.012 0.001 TYR C 92 ARG 0.003 0.000 ARG B 108 *********************** 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 132 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 96 time to evaluate : 1.610 Fit side-chains REVERT: A 315 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7494 (tp30) REVERT: B 315 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7493 (tp30) REVERT: C 315 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7494 (tp30) REVERT: D 315 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7493 (tp30) outliers start: 36 outliers final: 16 residues processed: 128 average time/residue: 1.1308 time to fit residues: 162.4064 Evaluate side-chains 112 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL 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 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 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 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 154 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 81 optimal weight: 0.0040 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 0.0050 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.7208 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14780 Z= 0.167 Angle : 0.519 5.882 20220 Z= 0.269 Chirality : 0.043 0.141 2052 Planarity : 0.004 0.033 2548 Dihedral : 4.517 34.032 2012 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.66 % Allowed : 12.77 % Favored : 84.57 % 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 (0.22), residues: 1716 helix: 1.46 (0.23), residues: 560 sheet: 0.26 (0.30), residues: 284 loop : 0.05 (0.24), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 243 HIS 0.001 0.000 HIS C 111 PHE 0.009 0.001 PHE C 394 TYR 0.010 0.001 TYR C 92 ARG 0.002 0.000 ARG B 86 *********************** 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 143 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 103 time to evaluate : 1.562 Fit side-chains REVERT: A 315 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: B 315 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7465 (tp30) REVERT: C 315 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: D 315 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7466 (tp30) outliers start: 40 outliers final: 20 residues processed: 135 average time/residue: 1.1940 time to fit residues: 178.8659 Evaluate side-chains 120 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 14780 Z= 0.460 Angle : 0.685 6.518 20220 Z= 0.362 Chirality : 0.052 0.151 2052 Planarity : 0.006 0.043 2548 Dihedral : 5.399 38.089 2012 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.33 % Allowed : 13.90 % 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: 0.41 (0.21), residues: 1716 helix: 1.28 (0.23), residues: 532 sheet: 0.03 (0.30), residues: 284 loop : -0.18 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 260 HIS 0.003 0.001 HIS A 58 PHE 0.015 0.003 PHE A 109 TYR 0.017 0.002 TYR C 92 ARG 0.006 0.001 ARG B 108 *********************** 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 127 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 92 time to evaluate : 1.554 Fit side-chains outliers start: 35 outliers final: 24 residues processed: 119 average time/residue: 1.1338 time to fit residues: 150.5265 Evaluate side-chains 116 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 305 MET 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 B residue 457 LEU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 305 MET 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 C residue 457 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 457 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 0.0970 chunk 41 optimal weight: 0.4980 chunk 166 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 160 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14780 Z= 0.150 Angle : 0.519 5.799 20220 Z= 0.269 Chirality : 0.043 0.140 2052 Planarity : 0.004 0.034 2548 Dihedral : 4.593 34.650 2012 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.66 % Allowed : 13.56 % 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: 0.61 (0.21), residues: 1716 helix: 1.37 (0.23), residues: 560 sheet: 0.12 (0.30), residues: 284 loop : -0.04 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 183 HIS 0.002 0.000 HIS C 111 PHE 0.010 0.001 PHE B 96 TYR 0.008 0.001 TYR D 92 ARG 0.001 0.000 ARG D 86 *********************** 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 140 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 100 time to evaluate : 1.465 Fit side-chains REVERT: A 315 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: A 461 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6968 (mtpm) REVERT: B 315 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7496 (tp30) REVERT: B 461 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6968 (mtpm) REVERT: C 315 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7496 (tp30) REVERT: C 461 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6971 (mtpm) REVERT: D 315 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7494 (tp30) REVERT: D 461 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6970 (mtpm) outliers start: 40 outliers final: 20 residues processed: 132 average time/residue: 1.2441 time to fit residues: 181.5700 Evaluate side-chains 123 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 A residue 457 LEU Chi-restraints excluded: chain A residue 461 LYS 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 B residue 457 LEU Chi-restraints excluded: chain B residue 461 LYS 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 C residue 457 LEU Chi-restraints excluded: chain C residue 461 LYS 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 Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 461 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14780 Z= 0.226 Angle : 0.561 6.024 20220 Z= 0.292 Chirality : 0.045 0.145 2052 Planarity : 0.005 0.035 2548 Dihedral : 4.806 35.170 2012 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.93 % Allowed : 13.76 % 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: 0.55 (0.21), residues: 1716 helix: 1.32 (0.23), residues: 560 sheet: 0.12 (0.30), residues: 284 loop : -0.09 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 223 HIS 0.002 0.001 HIS A 111 PHE 0.011 0.002 PHE B 96 TYR 0.011 0.001 TYR C 92 ARG 0.002 0.000 ARG B 303 *********************** 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 120 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 91 time to evaluate : 1.705 Fit side-chains REVERT: A 315 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7508 (tp30) REVERT: B 315 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7507 (tp30) REVERT: B 461 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6980 (mtpm) REVERT: C 315 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7507 (tp30) REVERT: D 315 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7507 (tp30) outliers start: 29 outliers final: 24 residues processed: 112 average time/residue: 1.1889 time to fit residues: 148.5036 Evaluate side-chains 120 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 91 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 A residue 457 LEU 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 B residue 457 LEU Chi-restraints excluded: chain B residue 461 LYS 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 C residue 457 LEU 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 Chi-restraints excluded: chain D residue 457 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 81 optimal weight: 0.0070 chunk 15 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 144 optimal weight: 0.4980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 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 0.021 14780 Z= 0.143 Angle : 0.509 5.788 20220 Z= 0.262 Chirality : 0.043 0.139 2052 Planarity : 0.004 0.034 2548 Dihedral : 4.363 32.185 2012 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.26 % Allowed : 14.43 % 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: 0.78 (0.22), residues: 1716 helix: 1.50 (0.23), residues: 560 sheet: 0.22 (0.30), residues: 284 loop : 0.07 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 183 HIS 0.001 0.000 HIS A 178 PHE 0.010 0.001 PHE B 96 TYR 0.008 0.001 TYR D 92 ARG 0.001 0.000 ARG D 86 *********************** 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 115 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 1.542 Fit side-chains REVERT: A 315 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7454 (tp30) REVERT: A 461 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6998 (mtpm) REVERT: B 315 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7453 (tp30) REVERT: C 315 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7455 (tp30) REVERT: C 461 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.7009 (mtpm) REVERT: D 315 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7453 (tp30) REVERT: D 461 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.7009 (mtpm) outliers start: 19 outliers final: 12 residues processed: 107 average time/residue: 1.2867 time to fit residues: 152.4727 Evaluate side-chains 114 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 461 LYS 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 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 C residue 461 LYS 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 Chi-restraints excluded: chain D residue 461 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 0.4980 chunk 153 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14780 Z= 0.189 Angle : 0.538 5.944 20220 Z= 0.279 Chirality : 0.044 0.145 2052 Planarity : 0.004 0.035 2548 Dihedral : 4.580 32.896 2012 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.80 % Allowed : 13.90 % 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: 0.71 (0.21), residues: 1716 helix: 1.42 (0.23), residues: 560 sheet: 0.22 (0.30), residues: 284 loop : 0.02 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 223 HIS 0.002 0.001 HIS C 111 PHE 0.010 0.002 PHE A 96 TYR 0.009 0.001 TYR C 92 ARG 0.002 0.000 ARG A 86 *********************** 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 fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 1.478 Fit side-chains REVERT: A 315 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: A 461 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6991 (mtpm) REVERT: B 315 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7465 (tp30) REVERT: C 315 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7466 (tp30) REVERT: C 461 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6995 (mtpm) REVERT: D 315 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7465 (tp30) REVERT: D 461 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6995 (mtpm) outliers start: 27 outliers final: 20 residues processed: 114 average time/residue: 1.1945 time to fit residues: 151.1801 Evaluate side-chains 118 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 SER 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 A residue 461 LYS Chi-restraints excluded: chain B residue 216 SER 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 216 SER 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 C residue 461 LYS Chi-restraints excluded: chain D residue 216 SER 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 Chi-restraints excluded: chain D residue 461 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14780 Z= 0.262 Angle : 0.587 6.138 20220 Z= 0.306 Chirality : 0.046 0.148 2052 Planarity : 0.005 0.035 2548 Dihedral : 4.911 34.861 2012 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.33 % Allowed : 13.43 % Favored : 84.24 % 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: 0.54 (0.21), residues: 1716 helix: 1.27 (0.23), residues: 560 sheet: 0.13 (0.30), residues: 284 loop : -0.07 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 260 HIS 0.002 0.001 HIS C 111 PHE 0.011 0.002 PHE B 96 TYR 0.012 0.001 TYR C 92 ARG 0.003 0.001 ARG A 303 ********************** 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 126 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 91 time to evaluate : 1.724 Fit side-chains REVERT: A 315 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7494 (tp30) REVERT: B 315 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7493 (tp30) REVERT: C 315 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: D 315 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7494 (tp30) outliers start: 35 outliers final: 24 residues processed: 118 average time/residue: 1.1456 time to fit residues: 151.0694 Evaluate side-chains 115 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 87 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 216 SER 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 216 SER 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 216 SER 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 216 SER 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 41 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 140 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.085565 restraints weight = 15749.945| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.49 r_work: 0.2778 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14780 Z= 0.201 Angle : 0.552 5.959 20220 Z= 0.286 Chirality : 0.044 0.146 2052 Planarity : 0.005 0.034 2548 Dihedral : 4.713 33.576 2012 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.86 % Allowed : 13.63 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.61 (0.21), residues: 1716 helix: 1.32 (0.23), residues: 560 sheet: 0.15 (0.30), residues: 284 loop : -0.02 (0.23), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 223 HIS 0.002 0.001 HIS D 111 PHE 0.011 0.002 PHE C 96 TYR 0.010 0.001 TYR C 92 ARG 0.002 0.000 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4140.47 seconds wall clock time: 74 minutes 24.76 seconds (4464.76 seconds total)