Starting phenix.real_space_refine on Wed Feb 21 23:29:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2024/7vvu_32148_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2024/7vvu_32148.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2024/7vvu_32148_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2024/7vvu_32148_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2024/7vvu_32148_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2024/7vvu_32148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2024/7vvu_32148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2024/7vvu_32148_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2024/7vvu_32148_updated.pdb" } resolution = 3.4 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 13019 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 362 5.49 5 S 36 5.16 5 C 11082 2.51 5 N 3536 2.21 5 O 4358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y GLU 24": "OE1" <-> "OE2" Residue "Y GLU 35": "OE1" <-> "OE2" Residue "Y TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 65": "OE1" <-> "OE2" Residue "T PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 187": "OD1" <-> "OD2" Residue "T PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 281": "OE1" <-> "OE2" Residue "T PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 316": "OE1" <-> "OE2" Residue "T ARG 318": "NH1" <-> "NH2" Residue "T ARG 324": "NH1" <-> "NH2" Residue "T GLU 355": "OE1" <-> "OE2" Residue "T GLU 387": "OE1" <-> "OE2" Residue "O TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 59": "OE1" <-> "OE2" Residue "O ASP 77": "OD1" <-> "OD2" Residue "O PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 52": "OE1" <-> "OE2" Residue "Q TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 56": "OE1" <-> "OE2" Residue "U TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 76": "OE1" <-> "OE2" Residue "U TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 105": "OE1" <-> "OE2" Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 56": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "P GLU 178": "OE1" <-> "OE2" Residue "P GLU 212": "OE1" <-> "OE2" Residue "P GLU 238": "OE1" <-> "OE2" Residue "P ARG 245": "NH1" <-> "NH2" Residue "P TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 331": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19374 Number of models: 1 Model: "" Number of chains: 16 Chain: "Y" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 396 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain: "V" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 923 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "T" Number of atoms: 2294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2294 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain: "O" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "S" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "U" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "A" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 774 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "N" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "P" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2286 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain: "W" Number of atoms: 3666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 3666 Classifications: {'DNA': 180} Link IDs: {'rna3p': 179} Chain: "I" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 3695 Classifications: {'DNA': 179} Link IDs: {'rna3p': 178} Chain: "X" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 82 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CMC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CMC:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 10.28, per 1000 atoms: 0.53 Number of scatterers: 19374 At special positions: 0 Unit cell: (123.405, 169.952, 182.942, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 362 15.00 O 4358 8.00 N 3536 7.00 C 11082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.98 Conformation dependent library (CDL) restraints added in 1.9 seconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2794 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 3 sheets defined 61.5% alpha, 2.7% beta 164 base pairs and 299 stacking pairs defined. Time for finding SS restraints: 8.96 Creating SS restraints... Processing helix chain 'Y' and resid 2 through 44 Processing helix chain 'V' and resid 3 through 15 Processing helix chain 'V' and resid 17 through 56 removed outlier: 3.905A pdb=" N LYS V 45 " --> pdb=" O LYS V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 65 through 112 Processing helix chain 'T' and resid 131 through 136 removed outlier: 4.352A pdb=" N ASP T 134 " --> pdb=" O ASN T 131 " (cutoff:3.500A) Processing helix chain 'T' and resid 155 through 157 No H-bonds generated for 'chain 'T' and resid 155 through 157' Processing helix chain 'T' and resid 166 through 175 Processing helix chain 'T' and resid 186 through 203 Processing helix chain 'T' and resid 207 through 209 No H-bonds generated for 'chain 'T' and resid 207 through 209' Processing helix chain 'T' and resid 211 through 213 No H-bonds generated for 'chain 'T' and resid 211 through 213' Processing helix chain 'T' and resid 217 through 226 Proline residue: T 222 - end of helix Processing helix chain 'T' and resid 229 through 241 removed outlier: 5.935A pdb=" N ASN T 233 " --> pdb=" O ALA T 230 " (cutoff:3.500A) Processing helix chain 'T' and resid 256 through 259 Processing helix chain 'T' and resid 264 through 285 removed outlier: 6.468A pdb=" N SER T 273 " --> pdb=" O GLU T 269 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LYS T 274 " --> pdb=" O LYS T 270 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR T 278 " --> pdb=" O LYS T 274 " (cutoff:3.500A) Processing helix chain 'T' and resid 314 through 316 No H-bonds generated for 'chain 'T' and resid 314 through 316' Processing helix chain 'T' and resid 328 through 382 removed outlier: 3.600A pdb=" N LEU T 334 " --> pdb=" O ASN T 330 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG T 335 " --> pdb=" O SER T 331 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA T 336 " --> pdb=" O GLN T 332 " (cutoff:3.500A) Processing helix chain 'T' and resid 389 through 391 No H-bonds generated for 'chain 'T' and resid 389 through 391' Processing helix chain 'O' and resid 45 through 56 Processing helix chain 'O' and resid 64 through 77 removed outlier: 4.027A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 113 Processing helix chain 'O' and resid 121 through 131 Processing helix chain 'Q' and resid 25 through 28 Processing helix chain 'Q' and resid 31 through 41 Processing helix chain 'Q' and resid 48 through 75 removed outlier: 3.850A pdb=" N TYR Q 51 " --> pdb=" O GLY Q 48 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU Q 52 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG Q 67 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 92 Processing helix chain 'S' and resid 17 through 21 Processing helix chain 'S' and resid 27 through 37 Processing helix chain 'S' and resid 45 through 73 removed outlier: 4.519A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 89 Processing helix chain 'S' and resid 91 through 96 Processing helix chain 'S' and resid 113 through 115 No H-bonds generated for 'chain 'S' and resid 113 through 115' Processing helix chain 'U' and resid 38 through 48 Processing helix chain 'U' and resid 56 through 83 Processing helix chain 'U' and resid 91 through 101 Processing helix chain 'U' and resid 104 through 122 Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 4.086A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 48 through 75 removed outlier: 3.694A pdb=" N TYR B 51 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 66 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'N' and resid 17 through 21 Processing helix chain 'N' and resid 27 through 37 Processing helix chain 'N' and resid 45 through 73 removed outlier: 4.519A pdb=" N VAL N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 89 Processing helix chain 'N' and resid 91 through 96 Processing helix chain 'N' and resid 113 through 115 No H-bonds generated for 'chain 'N' and resid 113 through 115' Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'P' and resid 187 through 190 No H-bonds generated for 'chain 'P' and resid 187 through 190' Processing helix chain 'P' and resid 208 through 217 Processing helix chain 'P' and resid 245 through 256 Processing helix chain 'P' and resid 309 through 311 No H-bonds generated for 'chain 'P' and resid 309 through 311' Processing helix chain 'P' and resid 316 through 330 Processing helix chain 'P' and resid 343 through 364 Processing helix chain 'P' and resid 370 through 377 Processing helix chain 'P' and resid 381 through 390 Processing helix chain 'P' and resid 407 through 419 Processing helix chain 'P' and resid 426 through 428 No H-bonds generated for 'chain 'P' and resid 426 through 428' Processing sheet with id= A, first strand: chain 'P' and resid 175 through 177 removed outlier: 6.308A pdb=" N ILE P 195 " --> pdb=" O ILE P 171 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'P' and resid 226 through 230 removed outlier: 3.847A pdb=" N ASN P 226 " --> pdb=" O GLU P 238 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE P 236 " --> pdb=" O ILE P 228 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG P 230 " --> pdb=" O VAL P 234 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL P 234 " --> pdb=" O ARG P 230 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY P 288 " --> pdb=" O MET P 276 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG P 278 " --> pdb=" O LEU P 286 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LEU P 286 " --> pdb=" O ARG P 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'P' and resid 394 through 396 663 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 423 hydrogen bonds 846 hydrogen bond angles 0 basepair planarities 164 basepair parallelities 299 stacking parallelities Total time for adding SS restraints: 8.26 Time building geometry restraints manager: 9.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4541 1.33 - 1.45: 5834 1.45 - 1.57: 9321 1.57 - 1.69: 721 1.69 - 1.81: 59 Bond restraints: 20476 Sorted by residual: bond pdb=" C3B CMC B 501 " pdb=" C4B CMC B 501 " ideal model delta sigma weight residual 1.347 1.526 -0.179 2.00e-02 2.50e+03 7.97e+01 bond pdb=" C9P CMC B 501 " pdb=" N8P CMC B 501 " ideal model delta sigma weight residual 1.485 1.327 0.158 2.00e-02 2.50e+03 6.25e+01 bond pdb=" C5P CMC B 501 " pdb=" N4P CMC B 501 " ideal model delta sigma weight residual 1.493 1.337 0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" C4B CMC B 501 " pdb=" O4B CMC B 501 " ideal model delta sigma weight residual 1.596 1.453 0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" C6A CMC B 501 " pdb=" N6A CMC B 501 " ideal model delta sigma weight residual 1.468 1.330 0.138 2.00e-02 2.50e+03 4.79e+01 ... (remaining 20471 not shown) Histogram of bond angle deviations from ideal: 97.32 - 104.66: 1370 104.66 - 112.00: 11087 112.00 - 119.34: 6357 119.34 - 126.67: 9282 126.67 - 134.01: 1087 Bond angle restraints: 29183 Sorted by residual: angle pdb=" C1B CMC B 501 " pdb=" N9A CMC B 501 " pdb=" C4A CMC B 501 " ideal model delta sigma weight residual 90.87 125.82 -34.95 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N1A CMC B 501 " pdb=" C6A CMC B 501 " pdb=" N6A CMC B 501 " ideal model delta sigma weight residual 94.05 118.84 -24.79 3.00e+00 1.11e-01 6.83e+01 angle pdb=" C5A CMC B 501 " pdb=" C6A CMC B 501 " pdb=" N6A CMC B 501 " ideal model delta sigma weight residual 145.98 123.89 22.09 3.00e+00 1.11e-01 5.42e+01 angle pdb=" C1B CMC B 501 " pdb=" N9A CMC B 501 " pdb=" C8A CMC B 501 " ideal model delta sigma weight residual 141.80 127.65 14.15 3.00e+00 1.11e-01 2.23e+01 angle pdb=" N ILE T 328 " pdb=" CA ILE T 328 " pdb=" C ILE T 328 " ideal model delta sigma weight residual 109.34 116.53 -7.19 2.08e+00 2.31e-01 1.20e+01 ... (remaining 29178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.89: 9519 31.89 - 63.77: 1833 63.77 - 95.66: 53 95.66 - 127.54: 4 127.54 - 159.43: 3 Dihedral angle restraints: 11412 sinusoidal: 7100 harmonic: 4312 Sorted by residual: dihedral pdb=" C4' DT I 15 " pdb=" C3' DT I 15 " pdb=" O3' DT I 15 " pdb=" P DC I 16 " ideal model delta sinusoidal sigma weight residual 220.00 60.57 159.43 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" C4' DG I 94 " pdb=" C3' DG I 94 " pdb=" O3' DG I 94 " pdb=" P DG I 95 " ideal model delta sinusoidal sigma weight residual 220.00 64.28 155.72 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DT W 15 " pdb=" C3' DT W 15 " pdb=" O3' DT W 15 " pdb=" P DG W 16 " ideal model delta sinusoidal sigma weight residual -140.00 -10.08 -129.92 1 3.50e+01 8.16e-04 1.29e+01 ... (remaining 11409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3071 0.088 - 0.177: 182 0.177 - 0.265: 7 0.265 - 0.353: 0 0.353 - 0.441: 1 Chirality restraints: 3261 Sorted by residual: chirality pdb=" C3B CMC B 501 " pdb=" C2B CMC B 501 " pdb=" C4B CMC B 501 " pdb=" O3B CMC B 501 " both_signs ideal model delta sigma weight residual False -2.35 -2.79 0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" C4' DG W 16 " pdb=" C5' DG W 16 " pdb=" O4' DG W 16 " pdb=" C3' DG W 16 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C1' DC W 11 " pdb=" O4' DC W 11 " pdb=" C2' DC W 11 " pdb=" N1 DC W 11 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3258 not shown) Planarity restraints: 2458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P CMC B 501 " -0.118 2.00e-02 2.50e+03 9.77e-02 1.19e+02 pdb=" C9P CMC B 501 " 0.029 2.00e-02 2.50e+03 pdb=" CAP CMC B 501 " -0.087 2.00e-02 2.50e+03 pdb=" N8P CMC B 501 " 0.159 2.00e-02 2.50e+03 pdb=" O9P CMC B 501 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE T 268 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C ILE T 268 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE T 268 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU T 269 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 154 " 0.019 2.00e-02 2.50e+03 1.87e-02 7.86e+00 pdb=" N1 DC I 154 " -0.045 2.00e-02 2.50e+03 pdb=" C2 DC I 154 " 0.024 2.00e-02 2.50e+03 pdb=" O2 DC I 154 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DC I 154 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 154 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 154 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DC I 154 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC I 154 " 0.008 2.00e-02 2.50e+03 ... (remaining 2455 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2546 2.75 - 3.29: 18547 3.29 - 3.83: 37578 3.83 - 4.36: 43655 4.36 - 4.90: 64523 Nonbonded interactions: 166849 Sorted by model distance: nonbonded pdb=" OH TYR P 233 " pdb=" OH TYR P 316 " model vdw 2.216 2.440 nonbonded pdb=" OH TYR T 147 " pdb=" O ARG P 428 " model vdw 2.218 2.440 nonbonded pdb=" N PHE T 141 " pdb=" O GLU P 281 " model vdw 2.224 2.520 nonbonded pdb=" OD2 ASP U 68 " pdb=" OH TYR B 98 " model vdw 2.254 2.440 nonbonded pdb=" O MET T 128 " pdb=" N GLU P 176 " model vdw 2.255 2.520 ... (remaining 166844 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'O' and resid 40 through 133) } ncs_group { reference = (chain 'B' and resid 22 through 101) selection = chain 'Q' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'S' } 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 11.510 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 56.990 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 0.006 0.179 20476 Z= 0.317 Angle : 0.754 34.954 29183 Z= 0.423 Chirality : 0.045 0.441 3261 Planarity : 0.005 0.098 2458 Dihedral : 24.883 159.430 8618 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.31 % Allowed : 3.24 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.22), residues: 1440 helix: 2.20 (0.16), residues: 938 sheet: -0.51 (0.82), residues: 39 loop : -0.75 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP P 247 HIS 0.006 0.001 HIS Q 75 PHE 0.010 0.001 PHE U 70 TYR 0.017 0.001 TYR P 265 ARG 0.006 0.001 ARG P 395 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 27 ASP cc_start: 0.9386 (m-30) cc_final: 0.9099 (m-30) REVERT: V 1 MET cc_start: 0.5044 (mmt) cc_final: 0.4047 (ppp) REVERT: V 14 VAL cc_start: 0.8930 (p) cc_final: 0.8730 (m) REVERT: T 240 HIS cc_start: 0.9370 (t70) cc_final: 0.9086 (m90) REVERT: T 319 HIS cc_start: 0.6083 (p-80) cc_final: 0.5227 (t70) REVERT: O 120 MET cc_start: 0.8674 (mtp) cc_final: 0.8183 (mtt) REVERT: Q 49 LEU cc_start: 0.9824 (mt) cc_final: 0.9194 (mt) REVERT: Q 88 TYR cc_start: 0.9037 (m-10) cc_final: 0.8714 (m-80) REVERT: S 110 ASN cc_start: 0.8589 (t0) cc_final: 0.7962 (t0) REVERT: A 90 MET cc_start: 0.9347 (mmm) cc_final: 0.8958 (mmm) REVERT: A 125 GLN cc_start: 0.9342 (mt0) cc_final: 0.9043 (mp10) REVERT: B 20 LYS cc_start: 0.3922 (OUTLIER) cc_final: 0.2833 (tppt) REVERT: B 53 GLU cc_start: 0.8988 (tp30) cc_final: 0.8681 (tp30) REVERT: B 84 MET cc_start: 0.8972 (mmm) cc_final: 0.8300 (mmm) REVERT: N 56 GLU cc_start: 0.9270 (tt0) cc_final: 0.8776 (tt0) REVERT: N 72 ASP cc_start: 0.8618 (m-30) cc_final: 0.8396 (m-30) REVERT: D 59 MET cc_start: 0.9355 (tpp) cc_final: 0.9017 (tpt) REVERT: P 252 CYS cc_start: 0.9507 (m) cc_final: 0.9169 (m) REVERT: P 254 LEU cc_start: 0.9777 (tp) cc_final: 0.9551 (mt) outliers start: 4 outliers final: 0 residues processed: 234 average time/residue: 0.3902 time to fit residues: 129.4386 Evaluate side-chains 130 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 48 GLN A 93 GLN B 18 HIS B 25 ASN P 414 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 20476 Z= 0.185 Angle : 0.579 11.589 29183 Z= 0.330 Chirality : 0.035 0.274 3261 Planarity : 0.004 0.036 2458 Dihedral : 29.260 170.518 5553 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.39 % Allowed : 7.78 % Favored : 90.83 % 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: 2.36 (0.22), residues: 1440 helix: 2.60 (0.17), residues: 932 sheet: -0.34 (0.83), residues: 39 loop : -0.44 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 353 HIS 0.004 0.001 HIS T 338 PHE 0.012 0.001 PHE V 95 TYR 0.015 0.001 TYR A 99 ARG 0.008 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 1 MET cc_start: 0.5132 (mmt) cc_final: 0.4172 (ppp) REVERT: T 240 HIS cc_start: 0.9419 (t70) cc_final: 0.9072 (m90) REVERT: T 294 GLN cc_start: 0.8306 (pm20) cc_final: 0.8063 (mp10) REVERT: T 319 HIS cc_start: 0.5893 (p-80) cc_final: 0.5070 (t70) REVERT: O 120 MET cc_start: 0.8582 (mtp) cc_final: 0.8174 (mtt) REVERT: Q 88 TYR cc_start: 0.8928 (m-10) cc_final: 0.8724 (m-80) REVERT: S 110 ASN cc_start: 0.8575 (t0) cc_final: 0.8000 (t0) REVERT: A 90 MET cc_start: 0.9296 (mmm) cc_final: 0.8953 (mmm) REVERT: A 125 GLN cc_start: 0.9316 (mt0) cc_final: 0.8987 (mp10) REVERT: B 27 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8932 (mm-40) REVERT: B 63 GLU cc_start: 0.8877 (tp30) cc_final: 0.8652 (tp30) REVERT: B 84 MET cc_start: 0.8979 (mmm) cc_final: 0.8300 (mmm) REVERT: B 93 GLN cc_start: 0.8458 (mp10) cc_final: 0.8042 (mp10) REVERT: N 56 GLU cc_start: 0.9267 (tt0) cc_final: 0.8674 (tt0) REVERT: N 104 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8564 (mm-40) REVERT: D 33 ARG cc_start: 0.7850 (mtt90) cc_final: 0.7205 (mmt-90) REVERT: D 76 GLU cc_start: 0.9171 (tp30) cc_final: 0.8551 (mm-30) REVERT: D 108 LYS cc_start: 0.9533 (mmmm) cc_final: 0.9327 (mmmm) REVERT: P 252 CYS cc_start: 0.9416 (m) cc_final: 0.9209 (m) REVERT: P 276 MET cc_start: 0.8744 (tmm) cc_final: 0.8475 (tmm) outliers start: 18 outliers final: 6 residues processed: 166 average time/residue: 0.2908 time to fit residues: 75.3096 Evaluate side-chains 144 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 40 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain P residue 246 THR Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 405 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 160 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 54 optimal weight: 0.5980 chunk 128 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 80 GLN B 18 HIS D 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20476 Z= 0.201 Angle : 0.556 9.034 29183 Z= 0.319 Chirality : 0.034 0.158 3261 Planarity : 0.004 0.037 2458 Dihedral : 29.179 171.632 5549 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.08 % Allowed : 9.09 % Favored : 89.83 % 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: 2.47 (0.22), residues: 1440 helix: 2.59 (0.17), residues: 945 sheet: 0.74 (1.01), residues: 27 loop : -0.34 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP P 353 HIS 0.004 0.001 HIS Y 46 PHE 0.018 0.001 PHE V 21 TYR 0.014 0.001 TYR V 42 ARG 0.004 0.000 ARG D 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 1 MET cc_start: 0.5135 (mmt) cc_final: 0.4276 (ppp) REVERT: T 164 MET cc_start: 0.5315 (mtt) cc_final: 0.4300 (mtt) REVERT: T 240 HIS cc_start: 0.9417 (t70) cc_final: 0.9053 (m90) REVERT: T 294 GLN cc_start: 0.8390 (pm20) cc_final: 0.8142 (mp10) REVERT: T 319 HIS cc_start: 0.5917 (p-80) cc_final: 0.5046 (t70) REVERT: O 120 MET cc_start: 0.8614 (mtp) cc_final: 0.8187 (mtt) REVERT: S 110 ASN cc_start: 0.8613 (t0) cc_final: 0.8097 (t0) REVERT: A 90 MET cc_start: 0.9341 (mmm) cc_final: 0.9033 (mmm) REVERT: A 105 GLU cc_start: 0.8821 (tp30) cc_final: 0.8572 (tp30) REVERT: A 120 MET cc_start: 0.8324 (mmm) cc_final: 0.7928 (mmm) REVERT: A 125 GLN cc_start: 0.9348 (mt0) cc_final: 0.8979 (mp10) REVERT: B 24 ASP cc_start: 0.8414 (p0) cc_final: 0.8159 (p0) REVERT: B 27 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8868 (mm-40) REVERT: B 53 GLU cc_start: 0.9001 (tp30) cc_final: 0.8711 (tp30) REVERT: B 84 MET cc_start: 0.8985 (mmm) cc_final: 0.8313 (mmm) REVERT: B 93 GLN cc_start: 0.8705 (mp10) cc_final: 0.8254 (mp10) REVERT: N 56 GLU cc_start: 0.9248 (tt0) cc_final: 0.8813 (tt0) REVERT: D 76 GLU cc_start: 0.9237 (tp30) cc_final: 0.8584 (mm-30) REVERT: P 247 TRP cc_start: 0.8556 (t60) cc_final: 0.7417 (t60) REVERT: P 252 CYS cc_start: 0.9489 (m) cc_final: 0.9277 (m) REVERT: P 353 TRP cc_start: 0.8964 (m-10) cc_final: 0.8649 (m-90) REVERT: P 379 MET cc_start: 0.8586 (tpp) cc_final: 0.8343 (tpp) outliers start: 14 outliers final: 9 residues processed: 147 average time/residue: 0.2899 time to fit residues: 67.0060 Evaluate side-chains 136 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 40 GLU Chi-restraints excluded: chain V residue 15 SER Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain P residue 251 LEU Chi-restraints excluded: chain P residue 405 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 141 optimal weight: 80.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20476 Z= 0.262 Angle : 0.581 11.542 29183 Z= 0.331 Chirality : 0.035 0.143 3261 Planarity : 0.004 0.039 2458 Dihedral : 29.336 171.393 5549 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.16 % Allowed : 9.94 % Favored : 88.91 % 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: 2.38 (0.22), residues: 1440 helix: 2.50 (0.17), residues: 939 sheet: 0.68 (1.06), residues: 27 loop : -0.28 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP P 353 HIS 0.009 0.001 HIS Y 46 PHE 0.059 0.001 PHE V 21 TYR 0.016 0.001 TYR V 42 ARG 0.005 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 1 MET cc_start: 0.4991 (mmt) cc_final: 0.4386 (ppp) REVERT: T 164 MET cc_start: 0.5359 (mtt) cc_final: 0.4700 (mtt) REVERT: T 294 GLN cc_start: 0.8655 (pm20) cc_final: 0.8397 (mp10) REVERT: T 319 HIS cc_start: 0.5957 (p-80) cc_final: 0.4925 (t70) REVERT: S 110 ASN cc_start: 0.8663 (t0) cc_final: 0.8208 (t0) REVERT: A 90 MET cc_start: 0.9375 (mmm) cc_final: 0.9072 (mmm) REVERT: A 105 GLU cc_start: 0.8888 (tp30) cc_final: 0.8486 (tp30) REVERT: A 120 MET cc_start: 0.8345 (mmm) cc_final: 0.7972 (mmm) REVERT: A 125 GLN cc_start: 0.9360 (mt0) cc_final: 0.8983 (mp10) REVERT: B 27 GLN cc_start: 0.9345 (mm-40) cc_final: 0.9110 (mm-40) REVERT: B 35 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9065 (mtt-85) REVERT: B 53 GLU cc_start: 0.9179 (tp30) cc_final: 0.8957 (tp30) REVERT: B 63 GLU cc_start: 0.9016 (tp30) cc_final: 0.8816 (tp30) REVERT: B 84 MET cc_start: 0.8997 (mmm) cc_final: 0.8356 (mmm) REVERT: N 56 GLU cc_start: 0.9177 (tt0) cc_final: 0.8746 (tt0) REVERT: D 33 ARG cc_start: 0.7841 (mtt90) cc_final: 0.7156 (mmt180) REVERT: D 76 GLU cc_start: 0.9292 (tp30) cc_final: 0.8585 (mm-30) REVERT: P 252 CYS cc_start: 0.9555 (m) cc_final: 0.9183 (m) REVERT: P 353 TRP cc_start: 0.9030 (m-10) cc_final: 0.8554 (m-90) REVERT: P 379 MET cc_start: 0.8784 (tpp) cc_final: 0.8564 (tpp) outliers start: 15 outliers final: 11 residues processed: 139 average time/residue: 0.3662 time to fit residues: 80.0152 Evaluate side-chains 137 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 40 GLU Chi-restraints excluded: chain T residue 198 HIS Chi-restraints excluded: chain T residue 395 LYS Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain P residue 286 LEU Chi-restraints excluded: chain P residue 405 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 126 optimal weight: 0.0870 chunk 70 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 117 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 240 HIS B 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20476 Z= 0.158 Angle : 0.536 10.642 29183 Z= 0.307 Chirality : 0.033 0.134 3261 Planarity : 0.004 0.044 2458 Dihedral : 29.095 175.844 5549 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.54 % Allowed : 10.63 % Favored : 88.83 % 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: 2.56 (0.22), residues: 1440 helix: 2.60 (0.17), residues: 944 sheet: 0.49 (1.01), residues: 27 loop : -0.12 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP P 353 HIS 0.009 0.001 HIS T 240 PHE 0.045 0.001 PHE V 21 TYR 0.015 0.001 TYR V 42 ARG 0.005 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 1 MET cc_start: 0.4903 (mmt) cc_final: 0.4353 (ppp) REVERT: T 319 HIS cc_start: 0.5922 (p-80) cc_final: 0.4984 (t70) REVERT: O 120 MET cc_start: 0.8536 (mtt) cc_final: 0.7802 (mtt) REVERT: S 110 ASN cc_start: 0.8640 (t0) cc_final: 0.8222 (t0) REVERT: A 90 MET cc_start: 0.9295 (mmm) cc_final: 0.8988 (mmm) REVERT: A 105 GLU cc_start: 0.8911 (tp30) cc_final: 0.8490 (tp30) REVERT: A 120 MET cc_start: 0.8338 (mmm) cc_final: 0.7967 (mmm) REVERT: A 125 GLN cc_start: 0.9326 (mt0) cc_final: 0.8939 (mp10) REVERT: B 24 ASP cc_start: 0.8485 (p0) cc_final: 0.8211 (p0) REVERT: B 53 GLU cc_start: 0.9117 (tp30) cc_final: 0.8911 (tp30) REVERT: B 84 MET cc_start: 0.8977 (mmm) cc_final: 0.8343 (mmm) REVERT: N 56 GLU cc_start: 0.9211 (tt0) cc_final: 0.8802 (tt0) REVERT: D 33 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7171 (mmt180) REVERT: D 35 GLU cc_start: 0.8430 (pp20) cc_final: 0.8077 (pp20) REVERT: D 76 GLU cc_start: 0.9210 (tp30) cc_final: 0.8573 (mm-30) REVERT: P 247 TRP cc_start: 0.8430 (t60) cc_final: 0.7697 (t60) REVERT: P 252 CYS cc_start: 0.9439 (m) cc_final: 0.9189 (m) REVERT: P 353 TRP cc_start: 0.9043 (m-10) cc_final: 0.8630 (m-90) outliers start: 7 outliers final: 5 residues processed: 138 average time/residue: 0.2820 time to fit residues: 62.3436 Evaluate side-chains 130 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 40 GLU Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain P residue 405 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 141 optimal weight: 50.0000 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 16 ASN B 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 20476 Z= 0.333 Angle : 0.607 10.122 29183 Z= 0.343 Chirality : 0.037 0.140 3261 Planarity : 0.004 0.038 2458 Dihedral : 29.341 179.157 5549 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.23 % Allowed : 11.09 % Favored : 87.67 % 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: 2.34 (0.22), residues: 1440 helix: 2.47 (0.17), residues: 936 sheet: 1.39 (0.88), residues: 31 loop : -0.34 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 247 HIS 0.004 0.001 HIS D 49 PHE 0.053 0.002 PHE V 21 TYR 0.021 0.002 TYR A 99 ARG 0.005 0.001 ARG T 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 1 MET cc_start: 0.5182 (mmt) cc_final: 0.4780 (ppp) REVERT: T 164 MET cc_start: 0.5872 (mtt) cc_final: 0.5011 (mtt) REVERT: T 319 HIS cc_start: 0.6077 (p-80) cc_final: 0.5024 (t70) REVERT: O 120 MET cc_start: 0.8390 (mtt) cc_final: 0.7645 (mtt) REVERT: Q 88 TYR cc_start: 0.9003 (m-10) cc_final: 0.8688 (m-80) REVERT: S 110 ASN cc_start: 0.8730 (t0) cc_final: 0.8352 (t0) REVERT: A 90 MET cc_start: 0.9409 (mmm) cc_final: 0.9093 (mmm) REVERT: A 105 GLU cc_start: 0.8902 (tp30) cc_final: 0.8571 (tp30) REVERT: A 120 MET cc_start: 0.8366 (mmm) cc_final: 0.8005 (mmm) REVERT: A 125 GLN cc_start: 0.9372 (mt0) cc_final: 0.9017 (mp10) REVERT: B 35 ARG cc_start: 0.9353 (OUTLIER) cc_final: 0.9051 (mtt-85) REVERT: B 63 GLU cc_start: 0.9152 (tp30) cc_final: 0.8861 (tp30) REVERT: B 84 MET cc_start: 0.8996 (mmm) cc_final: 0.8358 (mmm) REVERT: N 56 GLU cc_start: 0.9190 (tt0) cc_final: 0.8778 (tt0) REVERT: D 33 ARG cc_start: 0.7803 (mtt90) cc_final: 0.7195 (mmt180) REVERT: D 35 GLU cc_start: 0.8373 (pp20) cc_final: 0.8037 (pp20) REVERT: D 76 GLU cc_start: 0.9270 (tp30) cc_final: 0.8586 (mm-30) REVERT: P 252 CYS cc_start: 0.9509 (m) cc_final: 0.9246 (m) outliers start: 16 outliers final: 10 residues processed: 132 average time/residue: 0.3024 time to fit residues: 62.9413 Evaluate side-chains 128 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 29 PHE Chi-restraints excluded: chain Y residue 40 GLU Chi-restraints excluded: chain V residue 4 SER Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain N residue 38 ASN Chi-restraints excluded: chain N residue 87 VAL Chi-restraints excluded: chain P residue 405 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 104 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8014 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20476 Z= 0.167 Angle : 0.542 11.350 29183 Z= 0.309 Chirality : 0.033 0.165 3261 Planarity : 0.003 0.042 2458 Dihedral : 29.041 178.717 5549 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.54 % Allowed : 11.63 % Favored : 87.83 % 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: 2.53 (0.22), residues: 1440 helix: 2.62 (0.17), residues: 940 sheet: 1.14 (0.90), residues: 33 loop : -0.28 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 353 HIS 0.002 0.001 HIS P 222 PHE 0.048 0.001 PHE V 21 TYR 0.015 0.001 TYR V 42 ARG 0.003 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 1 MET cc_start: 0.5030 (mmt) cc_final: 0.4670 (ppp) REVERT: T 164 MET cc_start: 0.5973 (mtt) cc_final: 0.5087 (mtt) REVERT: T 319 HIS cc_start: 0.6115 (p-80) cc_final: 0.5023 (t70) REVERT: O 120 MET cc_start: 0.8482 (mtt) cc_final: 0.7752 (mtt) REVERT: Q 53 GLU cc_start: 0.9053 (tp30) cc_final: 0.8786 (tp30) REVERT: S 110 ASN cc_start: 0.8691 (t0) cc_final: 0.8340 (t0) REVERT: A 90 MET cc_start: 0.9328 (mmm) cc_final: 0.9036 (mmm) REVERT: A 105 GLU cc_start: 0.8894 (tp30) cc_final: 0.8546 (tp30) REVERT: A 120 MET cc_start: 0.8347 (mmm) cc_final: 0.7976 (mmm) REVERT: A 125 GLN cc_start: 0.9337 (mt0) cc_final: 0.8960 (mp10) REVERT: B 35 ARG cc_start: 0.9368 (OUTLIER) cc_final: 0.8947 (mtt-85) REVERT: B 63 GLU cc_start: 0.9016 (tp30) cc_final: 0.8763 (tp30) REVERT: N 56 GLU cc_start: 0.9247 (tt0) cc_final: 0.8769 (tt0) REVERT: D 33 ARG cc_start: 0.7725 (mtt90) cc_final: 0.7163 (mmt180) REVERT: D 76 GLU cc_start: 0.9227 (tp30) cc_final: 0.8563 (mm-30) REVERT: P 247 TRP cc_start: 0.8521 (t60) cc_final: 0.7956 (t60) REVERT: P 252 CYS cc_start: 0.9456 (m) cc_final: 0.9209 (m) outliers start: 7 outliers final: 5 residues processed: 128 average time/residue: 0.3007 time to fit residues: 60.6552 Evaluate side-chains 127 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 40 GLU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain P residue 172 MET Chi-restraints excluded: chain P residue 246 THR Chi-restraints excluded: chain P residue 405 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 258 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20476 Z= 0.175 Angle : 0.534 10.858 29183 Z= 0.305 Chirality : 0.033 0.149 3261 Planarity : 0.003 0.042 2458 Dihedral : 28.911 177.186 5549 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.62 % Allowed : 11.86 % Favored : 87.52 % 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: 2.64 (0.22), residues: 1440 helix: 2.69 (0.17), residues: 938 sheet: 1.31 (0.93), residues: 33 loop : -0.20 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 353 HIS 0.003 0.001 HIS P 222 PHE 0.041 0.001 PHE V 21 TYR 0.024 0.001 TYR A 99 ARG 0.002 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 28 ILE cc_start: 0.8694 (mm) cc_final: 0.8472 (mm) REVERT: T 164 MET cc_start: 0.6101 (mtt) cc_final: 0.5235 (mtt) REVERT: T 319 HIS cc_start: 0.6123 (OUTLIER) cc_final: 0.5032 (t70) REVERT: O 120 MET cc_start: 0.8386 (mtt) cc_final: 0.7608 (mtt) REVERT: Q 53 GLU cc_start: 0.9101 (tp30) cc_final: 0.8821 (tp30) REVERT: S 110 ASN cc_start: 0.8699 (t0) cc_final: 0.8372 (t0) REVERT: A 90 MET cc_start: 0.9306 (mmm) cc_final: 0.9034 (mmm) REVERT: A 105 GLU cc_start: 0.8897 (tp30) cc_final: 0.8601 (tp30) REVERT: A 120 MET cc_start: 0.8407 (mmm) cc_final: 0.8037 (mmm) REVERT: A 125 GLN cc_start: 0.9349 (mt0) cc_final: 0.8967 (mp10) REVERT: B 35 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.8987 (mtt-85) REVERT: B 63 GLU cc_start: 0.8986 (tp30) cc_final: 0.8747 (tp30) REVERT: B 84 MET cc_start: 0.8950 (mmm) cc_final: 0.8741 (mmm) REVERT: N 56 GLU cc_start: 0.9239 (tt0) cc_final: 0.8762 (tt0) REVERT: D 33 ARG cc_start: 0.7719 (mtt90) cc_final: 0.7055 (mmt180) REVERT: D 35 GLU cc_start: 0.8471 (pp20) cc_final: 0.8105 (pp20) REVERT: D 76 GLU cc_start: 0.9291 (tp30) cc_final: 0.8630 (mm-30) REVERT: P 247 TRP cc_start: 0.8449 (t60) cc_final: 0.8032 (t60) REVERT: P 252 CYS cc_start: 0.9456 (m) cc_final: 0.9221 (m) outliers start: 8 outliers final: 4 residues processed: 134 average time/residue: 0.3027 time to fit residues: 63.7551 Evaluate side-chains 127 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 40 GLU Chi-restraints excluded: chain V residue 70 LYS Chi-restraints excluded: chain T residue 319 HIS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain P residue 405 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 142 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 25 ASN P 285 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20476 Z= 0.355 Angle : 0.627 13.859 29183 Z= 0.353 Chirality : 0.038 0.214 3261 Planarity : 0.004 0.038 2458 Dihedral : 29.201 177.393 5549 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.92 % Allowed : 11.71 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.22), residues: 1440 helix: 2.30 (0.17), residues: 935 sheet: 1.35 (0.89), residues: 31 loop : -0.31 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 247 HIS 0.005 0.001 HIS D 49 PHE 0.051 0.002 PHE V 21 TYR 0.020 0.002 TYR A 99 ARG 0.005 0.000 ARG T 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 164 MET cc_start: 0.6306 (mtt) cc_final: 0.5647 (mtt) REVERT: T 319 HIS cc_start: 0.6357 (OUTLIER) cc_final: 0.5160 (t70) REVERT: O 120 MET cc_start: 0.8397 (mtt) cc_final: 0.7656 (mtt) REVERT: Q 53 GLU cc_start: 0.9212 (tp30) cc_final: 0.8977 (tp30) REVERT: Q 88 TYR cc_start: 0.8940 (m-10) cc_final: 0.8669 (m-80) REVERT: S 110 ASN cc_start: 0.8764 (t0) cc_final: 0.8438 (t0) REVERT: A 50 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: A 90 MET cc_start: 0.9403 (mmm) cc_final: 0.9098 (mmm) REVERT: A 105 GLU cc_start: 0.8881 (tp30) cc_final: 0.8574 (tp30) REVERT: A 120 MET cc_start: 0.8368 (mmm) cc_final: 0.8006 (mmm) REVERT: A 125 GLN cc_start: 0.9370 (mt0) cc_final: 0.9003 (mp10) REVERT: B 35 ARG cc_start: 0.9355 (OUTLIER) cc_final: 0.8987 (mtt-85) REVERT: B 63 GLU cc_start: 0.9136 (tp30) cc_final: 0.8854 (tp30) REVERT: N 56 GLU cc_start: 0.9169 (tt0) cc_final: 0.8752 (tt0) REVERT: D 33 ARG cc_start: 0.7474 (mtt90) cc_final: 0.7001 (mmt-90) REVERT: D 76 GLU cc_start: 0.9235 (tp30) cc_final: 0.8598 (mm-30) REVERT: P 247 TRP cc_start: 0.8468 (t60) cc_final: 0.7868 (t60) REVERT: P 252 CYS cc_start: 0.9541 (m) cc_final: 0.9300 (m) outliers start: 12 outliers final: 4 residues processed: 130 average time/residue: 0.3031 time to fit residues: 61.5927 Evaluate side-chains 121 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 29 PHE Chi-restraints excluded: chain Y residue 40 GLU Chi-restraints excluded: chain V residue 4 SER Chi-restraints excluded: chain T residue 319 HIS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain P residue 405 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 285 HIS ** P 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20476 Z= 0.253 Angle : 0.582 12.039 29183 Z= 0.330 Chirality : 0.035 0.299 3261 Planarity : 0.004 0.041 2458 Dihedral : 29.037 178.250 5549 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.62 % Allowed : 12.17 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.28 (0.22), residues: 1440 helix: 2.42 (0.17), residues: 931 sheet: 1.43 (0.89), residues: 31 loop : -0.31 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 353 HIS 0.004 0.001 HIS B 75 PHE 0.046 0.002 PHE V 21 TYR 0.029 0.001 TYR T 289 ARG 0.002 0.000 ARG T 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 164 MET cc_start: 0.6106 (mtt) cc_final: 0.5459 (mtt) REVERT: T 240 HIS cc_start: 0.9367 (t70) cc_final: 0.9045 (m-70) REVERT: T 319 HIS cc_start: 0.6387 (OUTLIER) cc_final: 0.5239 (t70) REVERT: O 120 MET cc_start: 0.8492 (mtt) cc_final: 0.7772 (mtt) REVERT: Q 53 GLU cc_start: 0.9185 (tp30) cc_final: 0.8931 (tp30) REVERT: Q 88 TYR cc_start: 0.8947 (m-10) cc_final: 0.8669 (m-80) REVERT: S 110 ASN cc_start: 0.8775 (t0) cc_final: 0.8483 (t0) REVERT: A 90 MET cc_start: 0.9370 (mmm) cc_final: 0.9069 (mmm) REVERT: A 105 GLU cc_start: 0.8900 (tp30) cc_final: 0.8575 (tp30) REVERT: A 120 MET cc_start: 0.8393 (mmm) cc_final: 0.7996 (mmm) REVERT: A 125 GLN cc_start: 0.9346 (mt0) cc_final: 0.8980 (mp10) REVERT: B 35 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.9037 (mtt-85) REVERT: B 63 GLU cc_start: 0.9044 (tp30) cc_final: 0.8813 (tp30) REVERT: N 56 GLU cc_start: 0.9155 (tt0) cc_final: 0.8653 (tt0) REVERT: D 33 ARG cc_start: 0.7470 (mtt90) cc_final: 0.7008 (mmt-90) REVERT: D 76 GLU cc_start: 0.9295 (tp30) cc_final: 0.8606 (mm-30) REVERT: D 101 LEU cc_start: 0.9477 (mm) cc_final: 0.9228 (mp) REVERT: P 247 TRP cc_start: 0.8552 (t60) cc_final: 0.8133 (t60) REVERT: P 252 CYS cc_start: 0.9573 (m) cc_final: 0.9321 (m) outliers start: 8 outliers final: 4 residues processed: 121 average time/residue: 0.2999 time to fit residues: 57.6469 Evaluate side-chains 121 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 40 GLU Chi-restraints excluded: chain T residue 319 HIS Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain P residue 333 LYS Chi-restraints excluded: chain P residue 405 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 58 optimal weight: 0.3980 chunk 143 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 261 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.080505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.046767 restraints weight = 124083.554| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.30 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20476 Z= 0.186 Angle : 0.557 11.573 29183 Z= 0.315 Chirality : 0.034 0.240 3261 Planarity : 0.004 0.043 2458 Dihedral : 28.817 176.705 5549 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.54 % Allowed : 12.33 % Favored : 87.13 % 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: 2.48 (0.22), residues: 1440 helix: 2.54 (0.17), residues: 938 sheet: 1.05 (0.90), residues: 33 loop : -0.17 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 353 HIS 0.003 0.000 HIS P 222 PHE 0.043 0.001 PHE V 21 TYR 0.023 0.001 TYR A 99 ARG 0.004 0.000 ARG T 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3501.47 seconds wall clock time: 64 minutes 45.32 seconds (3885.32 seconds total)