Starting phenix.real_space_refine on Fri Dec 8 08:06:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd6_4807/12_2023/6rd6_4807.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd6_4807/12_2023/6rd6_4807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd6_4807/12_2023/6rd6_4807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd6_4807/12_2023/6rd6_4807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd6_4807/12_2023/6rd6_4807.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rd6_4807/12_2023/6rd6_4807.pdb" } resolution = 2.75 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 4940 2.51 5 N 1289 2.21 5 O 1523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ASP 7": "OD1" <-> "OD2" Residue "2 GLU 14": "OE1" <-> "OE2" Residue "2 TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 187": "NH1" <-> "NH2" Residue "2 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 230": "OD1" <-> "OD2" Residue "2 PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 346": "NH1" <-> "NH2" Residue "2 TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 420": "OE1" <-> "OE2" Residue "2 ASP 426": "OD1" <-> "OD2" Residue "2 TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 18": "OD1" <-> "OD2" Residue "4 TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 44": "OD1" <-> "OD2" Residue "4 GLU 63": "OE1" <-> "OE2" Residue "4 ARG 83": "NH1" <-> "NH2" Residue "4 TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 120": "OD1" <-> "OD2" Residue "4 TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 159": "OE1" <-> "OE2" Residue "4 TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 192": "OE1" <-> "OE2" Residue "4 ASP 196": "OD1" <-> "OD2" Residue "4 GLU 201": "OE1" <-> "OE2" Residue "4 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 217": "OE1" <-> "OE2" Residue "4 GLU 224": "OE1" <-> "OE2" Residue "4 ASP 230": "OD1" <-> "OD2" Residue "4 ARG 231": "NH1" <-> "NH2" Residue "4 ARG 254": "NH1" <-> "NH2" Residue "4 TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 270": "OD1" <-> "OD2" Residue "7 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 25": "OD1" <-> "OD2" Residue "7 GLU 47": "OE1" <-> "OE2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 109": "OD1" <-> "OD2" Residue "7 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 117": "OD1" <-> "OD2" Residue "7 TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 164": "NH1" <-> "NH2" Residue "7 ARG 165": "NH1" <-> "NH2" Residue "7 ARG 166": "NH1" <-> "NH2" Residue "7 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 163": "OD1" <-> "OD2" Residue "P GLU 166": "OE1" <-> "OE2" Residue "P PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 191": "OD1" <-> "OD2" Residue "P PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 204": "OD1" <-> "OD2" Residue "P ARG 206": "NH1" <-> "NH2" Residue "P PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 41": "OD1" <-> "OD2" Residue "T GLU 47": "OE1" <-> "OE2" Residue "T ARG 49": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7758 Number of models: 1 Model: "" Number of chains: 10 Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "P" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 665 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "T" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 374 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 4, 'TRANS': 41} Chain: "2" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "4" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "7" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 4.42, per 1000 atoms: 0.57 Number of scatterers: 7758 At special positions: 0 Unit cell: (128.466, 75.816, 114.777, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 1523 8.00 N 1289 7.00 C 4940 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=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.4 seconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1962 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 5 sheets defined 71.2% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain '2' and resid 7 through 19 Processing helix chain '2' and resid 25 through 39 Processing helix chain '2' and resid 44 through 58 removed outlier: 3.760A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 77 Processing helix chain '2' and resid 80 through 87 Processing helix chain '2' and resid 87 through 95 Processing helix chain '2' and resid 96 through 98 No H-bonds generated for 'chain '2' and resid 96 through 98' Processing helix chain '2' and resid 99 through 113 Processing helix chain '2' and resid 117 through 131 Processing helix chain '2' and resid 136 through 150 Processing helix chain '2' and resid 154 through 168 Processing helix chain '2' and resid 171 through 186 Processing helix chain '2' and resid 189 through 199 removed outlier: 3.826A pdb=" N VAL 2 193 " --> pdb=" O ASP 2 189 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP 2 194 " --> pdb=" O LYS 2 190 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 206 through 220 removed outlier: 3.688A pdb=" N ALA 2 210 " --> pdb=" O SER 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 235 Processing helix chain '2' and resid 236 through 239 Processing helix chain '2' and resid 240 through 255 Processing helix chain '2' and resid 258 through 276 Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 281 through 296 Processing helix chain '2' and resid 300 through 321 Processing helix chain '2' and resid 323 through 341 Processing helix chain '2' and resid 345 through 357 removed outlier: 3.871A pdb=" N VAL 2 357 " --> pdb=" O VAL 2 353 " (cutoff:3.500A) Processing helix chain '2' and resid 383 through 387 Processing helix chain '2' and resid 396 through 409 removed outlier: 3.778A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 423 Processing helix chain '2' and resid 426 through 442 Processing helix chain '4' and resid 7 through 14 removed outlier: 3.719A pdb=" N LEU 4 11 " --> pdb=" O LYS 4 7 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 35 Processing helix chain '4' and resid 46 through 67 Proline residue: 4 64 - end of helix removed outlier: 3.800A pdb=" N HIS 4 67 " --> pdb=" O GLU 4 63 " (cutoff:3.500A) Processing helix chain '4' and resid 78 through 95 Processing helix chain '4' and resid 99 through 112 Processing helix chain '4' and resid 117 through 125 Processing helix chain '4' and resid 130 through 149 Processing helix chain '4' and resid 158 through 175 Processing helix chain '4' and resid 178 through 188 Processing helix chain '4' and resid 191 through 234 Processing helix chain '4' and resid 236 through 258 removed outlier: 3.978A pdb=" N ALA 4 258 " --> pdb=" O ARG 4 254 " (cutoff:3.500A) Processing helix chain '4' and resid 261 through 284 removed outlier: 3.570A pdb=" N ALA 4 284 " --> pdb=" O SER 4 280 " (cutoff:3.500A) Processing helix chain '7' and resid 63 through 70 removed outlier: 4.159A pdb=" N SER 7 70 " --> pdb=" O LEU 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 83 through 106 Processing helix chain '7' and resid 109 through 114 removed outlier: 3.690A pdb=" N THR 7 112 " --> pdb=" O ASP 7 109 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR 7 114 " --> pdb=" O THR 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 122 removed outlier: 3.703A pdb=" N ALA 7 122 " --> pdb=" O PHE 7 118 " (cutoff:3.500A) Processing helix chain '7' and resid 123 through 145 Processing helix chain '7' and resid 146 through 148 No H-bonds generated for 'chain '7' and resid 146 through 148' Processing helix chain '7' and resid 149 through 155 Processing helix chain '7' and resid 157 through 166 removed outlier: 3.636A pdb=" N TYR 7 161 " --> pdb=" O VAL 7 157 " (cutoff:3.500A) Processing helix chain '7' and resid 174 through 188 Processing helix chain 'P' and resid 163 through 175 Processing helix chain 'P' and resid 210 through 229 Processing helix chain 'T' and resid 44 through 49 Processing helix chain 'T' and resid 55 through 76 Proline residue: T 68 - end of helix Processing sheet with id=AA1, first strand: chain '2' and resid 78 through 79 Processing sheet with id=AA2, first strand: chain '2' and resid 358 through 359 Processing sheet with id=AA3, first strand: chain '2' and resid 368 through 372 removed outlier: 4.330A pdb=" N ILE 2 368 " --> pdb=" O VAL 2 379 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS 2 376 " --> pdb=" O ALA 2 412 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA 2 414 " --> pdb=" O LYS 2 376 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU 2 378 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL 2 416 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLN 2 380 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '7' and resid 36 through 41 Processing sheet with id=AA5, first strand: chain 'P' and resid 183 through 190 removed outlier: 4.179A pdb=" N ARG P 205 " --> pdb=" O PHE P 202 " (cutoff:3.500A) 551 hydrogen bonds defined for protein. 1629 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2476 1.34 - 1.46: 1086 1.46 - 1.57: 4288 1.57 - 1.69: 0 1.69 - 1.81: 9 Bond restraints: 7859 Sorted by residual: bond pdb=" C GLN 4 51 " pdb=" N LEU 4 52 " ideal model delta sigma weight residual 1.335 1.438 -0.103 1.36e-02 5.41e+03 5.75e+01 bond pdb=" C ILE T 67 " pdb=" N PRO T 68 " ideal model delta sigma weight residual 1.336 1.379 -0.044 1.23e-02 6.61e+03 1.27e+01 bond pdb=" N ILE 4 49 " pdb=" CA ILE 4 49 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.36e+00 bond pdb=" C VAL 7 158 " pdb=" N PRO 7 159 " ideal model delta sigma weight residual 1.334 1.393 -0.060 2.34e-02 1.83e+03 6.47e+00 bond pdb=" N ASP 4 44 " pdb=" CA ASP 4 44 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.17e-02 7.31e+03 6.38e+00 ... (remaining 7854 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.13: 166 107.13 - 113.85: 4563 113.85 - 120.58: 3256 120.58 - 127.31: 2614 127.31 - 134.03: 53 Bond angle restraints: 10652 Sorted by residual: angle pdb=" C VAL 7 157 " pdb=" N VAL 7 158 " pdb=" CA VAL 7 158 " ideal model delta sigma weight residual 120.33 125.51 -5.18 8.00e-01 1.56e+00 4.18e+01 angle pdb=" CA GLN 4 51 " pdb=" C GLN 4 51 " pdb=" N LEU 4 52 " ideal model delta sigma weight residual 117.63 123.49 -5.86 1.25e+00 6.40e-01 2.20e+01 angle pdb=" C SER 4 6 " pdb=" N LYS 4 7 " pdb=" CA LYS 4 7 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" CA TYR 4 210 " pdb=" CB TYR 4 210 " pdb=" CG TYR 4 210 " ideal model delta sigma weight residual 113.90 121.83 -7.93 1.80e+00 3.09e-01 1.94e+01 angle pdb=" C TYR 2 345 " pdb=" N ARG 2 346 " pdb=" CA ARG 2 346 " ideal model delta sigma weight residual 120.09 125.19 -5.10 1.25e+00 6.40e-01 1.67e+01 ... (remaining 10647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 4374 17.70 - 35.41: 334 35.41 - 53.11: 44 53.11 - 70.81: 16 70.81 - 88.52: 7 Dihedral angle restraints: 4775 sinusoidal: 1747 harmonic: 3028 Sorted by residual: dihedral pdb=" CA LYS P 193 " pdb=" C LYS P 193 " pdb=" N LEU P 194 " pdb=" CA LEU P 194 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LEU P 162 " pdb=" C LEU P 162 " pdb=" N ASP P 163 " pdb=" CA ASP P 163 " ideal model delta harmonic sigma weight residual 180.00 160.73 19.27 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LEU 2 299 " pdb=" C LEU 2 299 " pdb=" N PRO 2 300 " pdb=" CA PRO 2 300 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 4772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 972 0.048 - 0.096: 209 0.096 - 0.144: 59 0.144 - 0.192: 11 0.192 - 0.240: 2 Chirality restraints: 1253 Sorted by residual: chirality pdb=" CG LEU 2 424 " pdb=" CB LEU 2 424 " pdb=" CD1 LEU 2 424 " pdb=" CD2 LEU 2 424 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA THR 2 391 " pdb=" N THR 2 391 " pdb=" C THR 2 391 " pdb=" CB THR 2 391 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA ALA 4 45 " pdb=" N ALA 4 45 " pdb=" C ALA 4 45 " pdb=" CB ALA 4 45 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 1250 not shown) Planarity restraints: 1357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER 2 99 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO 2 100 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO 2 100 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO 2 100 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR 2 391 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO 2 392 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO 2 392 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO 2 392 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 2 299 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO 2 300 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO 2 300 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO 2 300 " 0.032 5.00e-02 4.00e+02 ... (remaining 1354 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2462 2.82 - 3.34: 7184 3.34 - 3.86: 13238 3.86 - 4.38: 15197 4.38 - 4.90: 26175 Nonbonded interactions: 64256 Sorted by model distance: nonbonded pdb=" O GLY 7 180 " pdb=" OG1 THR 7 183 " model vdw 2.306 2.440 nonbonded pdb=" OH TYR 4 84 " pdb=" OH TYR 7 161 " model vdw 2.316 2.440 nonbonded pdb=" OD2 ASP 2 316 " pdb=" OG1 THR 4 41 " model vdw 2.323 2.440 nonbonded pdb=" O LYS T 52 " pdb=" O HOH T 601 " model vdw 2.337 2.440 nonbonded pdb=" O LYS P 189 " pdb=" O HOH P 301 " model vdw 2.345 2.440 ... (remaining 64251 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 7.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 24.140 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.050 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 0.103 7859 Z= 0.368 Angle : 0.819 10.478 10652 Z= 0.493 Chirality : 0.046 0.240 1253 Planarity : 0.008 0.062 1357 Dihedral : 13.672 88.518 2813 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.38 % Allowed : 4.19 % Favored : 95.43 % 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: -3.09 (0.20), residues: 1025 helix: -2.01 (0.14), residues: 705 sheet: -0.50 (0.72), residues: 61 loop : -1.90 (0.31), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP 7 107 HIS 0.009 0.002 HIS 4 232 PHE 0.014 0.002 PHE P 218 TYR 0.026 0.002 TYR 4 210 ARG 0.003 0.001 ARG 2 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 0.892 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 129 average time/residue: 1.2300 time to fit residues: 168.0697 Evaluate side-chains 83 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 68 ASN 2 74 ASN 2 122 ASN 2 243 GLN ** 4 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 239 GLN 7 60 GLN 7 123 HIS 7 170 HIS 7 184 ASN P 220 ASN P 223 ASN T 60 GLN T 64 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7859 Z= 0.215 Angle : 0.509 6.806 10652 Z= 0.271 Chirality : 0.038 0.135 1253 Planarity : 0.005 0.048 1357 Dihedral : 4.282 19.232 1092 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.54 % Allowed : 9.39 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.25), residues: 1025 helix: 0.48 (0.18), residues: 708 sheet: -0.05 (0.71), residues: 61 loop : -1.28 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 PHE 0.012 0.001 PHE 4 161 TYR 0.028 0.002 TYR 4 210 ARG 0.006 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.936 Fit side-chains outliers start: 20 outliers final: 6 residues processed: 103 average time/residue: 1.2488 time to fit residues: 136.3256 Evaluate side-chains 89 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 83 time to evaluate : 0.863 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.5462 time to fit residues: 3.0114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN 4 110 GLN ** 4 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7859 Z= 0.237 Angle : 0.507 8.013 10652 Z= 0.266 Chirality : 0.039 0.134 1253 Planarity : 0.004 0.044 1357 Dihedral : 4.087 17.850 1092 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.16 % Allowed : 11.42 % Favored : 86.42 % 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: 1.02 (0.26), residues: 1025 helix: 1.29 (0.19), residues: 716 sheet: 0.40 (0.73), residues: 57 loop : -0.93 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 4 205 HIS 0.005 0.001 HIS 7 123 PHE 0.012 0.002 PHE 4 161 TYR 0.027 0.002 TYR 4 210 ARG 0.004 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.860 Fit side-chains outliers start: 17 outliers final: 6 residues processed: 96 average time/residue: 1.4037 time to fit residues: 142.3139 Evaluate side-chains 96 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.7928 time to fit residues: 2.8870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.0570 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 0.0050 chunk 26 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 overall best weight: 0.4712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN ** 4 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7859 Z= 0.162 Angle : 0.459 7.359 10652 Z= 0.241 Chirality : 0.037 0.126 1253 Planarity : 0.004 0.043 1357 Dihedral : 3.891 16.391 1092 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.90 % Allowed : 12.56 % Favored : 85.53 % 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: 1.67 (0.26), residues: 1025 helix: 1.76 (0.19), residues: 718 sheet: 1.06 (0.74), residues: 57 loop : -0.75 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 PHE 0.010 0.001 PHE P 218 TYR 0.024 0.001 TYR 4 210 ARG 0.004 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.804 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 106 average time/residue: 1.1967 time to fit residues: 134.7084 Evaluate side-chains 100 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.863 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.5555 time to fit residues: 3.0041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN ** 4 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7859 Z= 0.187 Angle : 0.475 7.293 10652 Z= 0.247 Chirality : 0.038 0.129 1253 Planarity : 0.004 0.042 1357 Dihedral : 3.843 17.419 1092 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.79 % Allowed : 13.07 % Favored : 84.14 % 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: 1.96 (0.26), residues: 1025 helix: 1.95 (0.19), residues: 719 sheet: 1.36 (0.76), residues: 57 loop : -0.62 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 PHE 0.010 0.001 PHE P 218 TYR 0.024 0.002 TYR 4 210 ARG 0.004 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.876 Fit side-chains outliers start: 22 outliers final: 9 residues processed: 109 average time/residue: 1.5017 time to fit residues: 172.9991 Evaluate side-chains 89 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.0982 time to fit residues: 1.6122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 95 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN 4 232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7859 Z= 0.207 Angle : 0.478 7.582 10652 Z= 0.249 Chirality : 0.038 0.130 1253 Planarity : 0.004 0.041 1357 Dihedral : 3.853 15.860 1092 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.28 % Allowed : 13.96 % Favored : 83.76 % 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: 2.08 (0.26), residues: 1025 helix: 2.00 (0.19), residues: 720 sheet: 1.67 (0.78), residues: 57 loop : -0.55 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 PHE 0.011 0.001 PHE P 218 TYR 0.025 0.002 TYR 4 210 ARG 0.004 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.931 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 95 average time/residue: 1.3887 time to fit residues: 139.2343 Evaluate side-chains 99 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.4782 time to fit residues: 3.4007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 0.0870 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN 7 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7859 Z= 0.196 Angle : 0.484 7.985 10652 Z= 0.251 Chirality : 0.038 0.129 1253 Planarity : 0.004 0.041 1357 Dihedral : 3.835 16.087 1092 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.65 % Allowed : 14.97 % Favored : 83.38 % 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: 2.18 (0.26), residues: 1025 helix: 2.07 (0.19), residues: 720 sheet: 1.73 (0.77), residues: 58 loop : -0.48 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 PHE 0.011 0.001 PHE P 218 TYR 0.024 0.002 TYR 4 210 ARG 0.004 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.951 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 106 average time/residue: 1.3419 time to fit residues: 150.4586 Evaluate side-chains 89 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.1327 time to fit residues: 1.6194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 0.0170 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.9424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7859 Z= 0.252 Angle : 0.518 8.160 10652 Z= 0.267 Chirality : 0.039 0.133 1253 Planarity : 0.004 0.041 1357 Dihedral : 3.898 16.270 1092 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.65 % Allowed : 15.86 % Favored : 82.49 % 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: 2.13 (0.26), residues: 1025 helix: 2.03 (0.19), residues: 719 sheet: 1.77 (0.77), residues: 58 loop : -0.49 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 4 205 HIS 0.005 0.001 HIS 7 123 PHE 0.011 0.002 PHE P 218 TYR 0.025 0.002 TYR 4 210 ARG 0.003 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.881 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 92 average time/residue: 1.4081 time to fit residues: 136.8233 Evaluate side-chains 93 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.0908 time to fit residues: 1.4785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN 7 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7859 Z= 0.208 Angle : 0.496 8.274 10652 Z= 0.257 Chirality : 0.038 0.129 1253 Planarity : 0.004 0.042 1357 Dihedral : 3.846 15.601 1092 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.40 % Allowed : 16.24 % Favored : 82.36 % 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: 2.26 (0.26), residues: 1025 helix: 2.12 (0.19), residues: 719 sheet: 1.84 (0.77), residues: 58 loop : -0.44 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 PHE 0.011 0.001 PHE P 218 TYR 0.024 0.002 TYR 4 210 ARG 0.003 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 1.001 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 90 average time/residue: 1.4420 time to fit residues: 137.0822 Evaluate side-chains 88 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.6255 time to fit residues: 3.2836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 0.0070 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 74 optimal weight: 0.0030 chunk 11 optimal weight: 0.6980 overall best weight: 0.3006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN 7 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7859 Z= 0.146 Angle : 0.461 8.015 10652 Z= 0.237 Chirality : 0.037 0.124 1253 Planarity : 0.004 0.043 1357 Dihedral : 3.714 15.326 1092 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.27 % Allowed : 16.75 % Favored : 81.98 % 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 (0.27), residues: 1025 helix: 2.28 (0.19), residues: 720 sheet: 1.98 (0.77), residues: 58 loop : -0.37 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 4 205 HIS 0.003 0.001 HIS 4 232 PHE 0.011 0.001 PHE P 218 TYR 0.022 0.001 TYR 4 210 ARG 0.004 0.000 ARG P 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.872 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 89 average time/residue: 1.3113 time to fit residues: 123.4639 Evaluate side-chains 86 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.2290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 74 ASN 7 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.094307 restraints weight = 9468.746| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.77 r_work: 0.2923 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7859 Z= 0.217 Angle : 0.488 8.265 10652 Z= 0.252 Chirality : 0.038 0.129 1253 Planarity : 0.004 0.042 1357 Dihedral : 3.766 15.380 1092 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.14 % Allowed : 17.39 % Favored : 81.47 % 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: 2.41 (0.26), residues: 1025 helix: 2.21 (0.19), residues: 719 sheet: 2.06 (0.77), residues: 58 loop : -0.38 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 4 205 HIS 0.004 0.001 HIS 4 232 PHE 0.011 0.001 PHE P 218 TYR 0.024 0.002 TYR 4 210 ARG 0.004 0.000 ARG P 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3297.13 seconds wall clock time: 59 minutes 37.04 seconds (3577.04 seconds total)