Starting phenix.real_space_refine (version: dev) on Tue Feb 28 07:09:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2023/7vvu_32148_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2023/7vvu_32148.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2023/7vvu_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_2023/7vvu_32148_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2023/7vvu_32148_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2023/7vvu_32148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2023/7vvu_32148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2023/7vvu_32148_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vvu_32148/02_2023/7vvu_32148_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 10.84, per 1000 atoms: 0.56 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: 10.37 Conformation dependent library (CDL) restraints added in 1.8 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: 8.19 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: 8.80 Time building geometry restraints manager: 10.77 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: 9270 31.89 - 63.77: 1778 63.77 - 95.66: 53 95.66 - 127.54: 4 127.54 - 159.43: 3 Dihedral angle restraints: 11108 sinusoidal: 6796 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 11105 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 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. 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: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.010 Extract box with map and model: 12.260 Check model and map are aligned: 0.290 Process input model: 59.020 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.190 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 : 24.835 159.430 8314 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 % 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 *********************** 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 : 1.799 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 outliers start: 4 outliers final: 0 residues processed: 234 average time/residue: 0.3977 time to fit residues: 131.7418 Evaluate side-chains 120 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.854 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 45 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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: 0.8020 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 20476 Z= 0.221 Angle : 0.598 11.182 29183 Z= 0.338 Chirality : 0.036 0.277 3261 Planarity : 0.004 0.035 2458 Dihedral : 29.672 170.090 5245 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 1.54 % 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: 2.30 (0.22), residues: 1440 helix: 2.55 (0.17), residues: 933 sheet: 0.77 (0.98), residues: 27 loop : -0.55 (0.26), residues: 480 *********************** 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 166 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 155 average time/residue: 0.3091 time to fit residues: 75.6910 Evaluate side-chains 130 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 2.002 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1868 time to fit residues: 4.1753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 142 optimal weight: 30.0000 chunk 158 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** B 18 HIS D 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 20476 Z= 0.226 Angle : 0.571 10.689 29183 Z= 0.326 Chirality : 0.035 0.154 3261 Planarity : 0.004 0.037 2458 Dihedral : 29.588 171.824 5245 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 0.92 % 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: 2.40 (0.22), residues: 1440 helix: 2.55 (0.17), residues: 937 sheet: 0.79 (1.04), residues: 27 loop : -0.35 (0.26), residues: 476 *********************** 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 149 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 143 average time/residue: 0.3068 time to fit residues: 69.7159 Evaluate side-chains 125 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.711 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1810 time to fit residues: 3.4867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 83 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 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: 100.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.8062 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 20476 Z= 0.261 Angle : 0.588 11.432 29183 Z= 0.334 Chirality : 0.035 0.142 3261 Planarity : 0.004 0.042 2458 Dihedral : 29.630 171.755 5245 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 1.31 % 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: 2.24 (0.22), residues: 1440 helix: 2.34 (0.17), residues: 948 sheet: 0.59 (1.04), residues: 27 loop : -0.27 (0.27), residues: 465 *********************** 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 146 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 140 average time/residue: 0.3095 time to fit residues: 67.9205 Evaluate side-chains 125 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2157 time to fit residues: 4.9816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 70 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8032 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 20476 Z= 0.175 Angle : 0.553 10.997 29183 Z= 0.315 Chirality : 0.034 0.133 3261 Planarity : 0.004 0.045 2458 Dihedral : 29.505 175.857 5245 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 0.46 % 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: 2.34 (0.22), residues: 1440 helix: 2.42 (0.17), residues: 946 sheet: 1.26 (1.03), residues: 27 loop : -0.26 (0.27), residues: 467 *********************** 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 137 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 136 average time/residue: 0.2905 time to fit residues: 62.9739 Evaluate side-chains 120 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 1.718 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1591 time to fit residues: 2.7697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 41 optimal weight: 20.0000 chunk 170 optimal weight: 3.9990 chunk 141 optimal weight: 50.0000 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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: 0.8090 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 20476 Z= 0.302 Angle : 0.602 9.990 29183 Z= 0.341 Chirality : 0.036 0.129 3261 Planarity : 0.004 0.039 2458 Dihedral : 29.724 179.532 5245 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 0.92 % 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: 2.23 (0.22), residues: 1440 helix: 2.32 (0.17), residues: 939 sheet: 0.88 (0.90), residues: 33 loop : -0.22 (0.28), residues: 468 *********************** 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 131 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 126 average time/residue: 0.2942 time to fit residues: 60.1085 Evaluate side-chains 122 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.867 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1760 time to fit residues: 4.3092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 124 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 20476 Z= 0.223 Angle : 0.573 11.951 29183 Z= 0.325 Chirality : 0.034 0.142 3261 Planarity : 0.004 0.042 2458 Dihedral : 29.568 178.242 5245 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.46 % 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: 2.27 (0.22), residues: 1440 helix: 2.36 (0.17), residues: 937 sheet: 0.91 (0.89), residues: 33 loop : -0.22 (0.27), residues: 470 *********************** 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 128 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 125 average time/residue: 0.2803 time to fit residues: 57.4571 Evaluate side-chains 117 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 1.750 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2135 time to fit residues: 3.5968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 115 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 245 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3771 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= 0.207 Angle : 0.570 11.368 29183 Z= 0.322 Chirality : 0.034 0.145 3261 Planarity : 0.004 0.041 2458 Dihedral : 29.470 176.261 5245 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.30 (0.22), residues: 1440 helix: 2.36 (0.17), residues: 945 sheet: 0.89 (0.91), residues: 33 loop : -0.18 (0.27), residues: 462 *********************** 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 121 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 120 average time/residue: 0.3009 time to fit residues: 59.0066 Evaluate side-chains 114 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.704 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1654 time to fit residues: 2.4017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 68 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 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: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 16 ASN ** V 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 25 ASN P 285 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 20476 Z= 0.339 Angle : 0.641 13.582 29183 Z= 0.359 Chirality : 0.037 0.187 3261 Planarity : 0.004 0.039 2458 Dihedral : 29.685 176.683 5245 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.46 % 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: 2.02 (0.22), residues: 1440 helix: 2.17 (0.17), residues: 935 sheet: 1.03 (0.90), residues: 31 loop : -0.31 (0.27), residues: 474 *********************** 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 121 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 118 average time/residue: 0.2985 time to fit residues: 57.2684 Evaluate side-chains 114 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 1.703 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1881 time to fit residues: 4.0664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 79 optimal weight: 4.9990 chunk 116 optimal weight: 0.0770 chunk 175 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 0.5980 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4196 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= 0.192 Angle : 0.586 13.326 29183 Z= 0.329 Chirality : 0.034 0.144 3261 Planarity : 0.004 0.041 2458 Dihedral : 29.496 176.885 5245 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 0.15 % 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: 2.29 (0.22), residues: 1440 helix: 2.37 (0.17), residues: 934 sheet: 0.85 (0.91), residues: 33 loop : -0.16 (0.28), residues: 473 ********************** 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 123 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 122 average time/residue: 0.2940 time to fit residues: 58.4696 Evaluate side-chains 112 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.738 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2117 time to fit residues: 2.6526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 128 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 139 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 48 GLN ** V 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 285 HIS ** P 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.081507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.047207 restraints weight = 149912.785| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 5.08 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 20476 Z= 0.208 Angle : 0.585 12.868 29183 Z= 0.329 Chirality : 0.034 0.151 3261 Planarity : 0.004 0.041 2458 Dihedral : 29.425 179.248 5245 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.33 (0.22), residues: 1440 helix: 2.38 (0.17), residues: 936 sheet: 1.26 (0.92), residues: 31 loop : -0.14 (0.28), residues: 473 =============================================================================== Job complete usr+sys time: 3364.36 seconds wall clock time: 62 minutes 43.00 seconds (3763.00 seconds total)