Starting phenix.real_space_refine on Wed Feb 14 10:16:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxd_24729/02_2024/7rxd_24729.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxd_24729/02_2024/7rxd_24729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxd_24729/02_2024/7rxd_24729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxd_24729/02_2024/7rxd_24729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxd_24729/02_2024/7rxd_24729.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxd_24729/02_2024/7rxd_24729.pdb" } resolution = 3.6 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= 0.004 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 31 5.16 5 C 5749 2.51 5 N 1490 2.21 5 O 1737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 66": "OD1" <-> "OD2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "B ASP 526": "OD1" <-> "OD2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 166": "OE1" <-> "OE2" Residue "L ASP 175": "OD1" <-> "OD2" Residue "L TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 200": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 62": "OD1" <-> "OD2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 427": "OD1" <-> "OD2" Residue "R PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 471": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9007 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3433 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 24, 'TRANS': 414} Chain breaks: 4 Chain: "H" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1582 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 192} Chain breaks: 2 Chain: "L" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1588 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 194} Chain breaks: 2 Chain: "N" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 990 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1391 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 2 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.14, per 1000 atoms: 0.57 Number of scatterers: 9007 At special positions: 0 Unit cell: (118.72, 133.56, 111.3, 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 31 16.00 O 1737 8.00 N 1490 7.00 C 5749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.05 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 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 Links applied ALPHA1-4 " GLC A 1 " - " GLC A 2 " Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.8 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 22 sheets defined 27.9% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'B' and resid 17 through 28 Processing helix chain 'B' and resid 43 through 52 Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 64 through 74 removed outlier: 4.055A pdb=" N PHE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 89 Processing helix chain 'B' and resid 91 through 98 removed outlier: 3.553A pdb=" N TRP B 95 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 removed outlier: 4.490A pdb=" N ALA B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.923A pdb=" N THR B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 182 through 185 removed outlier: 4.399A pdb=" N ASP B 185 " --> pdb=" O VAL B 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 185' Processing helix chain 'B' and resid 186 through 202 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.640A pdb=" N ASP B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 336 through 353 removed outlier: 3.913A pdb=" N PHE B 340 " --> pdb=" O GLN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 370 removed outlier: 3.610A pdb=" N MET B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 391 through 406 Processing helix chain 'B' and resid 502 through 517 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.568A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.798A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 89 Processing helix chain 'L' and resid 126 through 133 Processing helix chain 'L' and resid 188 through 194 removed outlier: 3.722A pdb=" N HIS L 194 " --> pdb=" O ASP L 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.531A pdb=" N LYS N 65 " --> pdb=" O ASP N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 337 through 343 removed outlier: 3.748A pdb=" N VAL R 341 " --> pdb=" O PRO R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.798A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.935A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'B' and resid 37 through 39 removed outlier: 5.958A pdb=" N ILE B 10 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 9 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE B 62 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP B 11 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA B 265 " --> pdb=" O PRO B 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 39 removed outlier: 5.958A pdb=" N ILE B 10 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 9 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE B 62 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP B 11 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AA4, first strand: chain 'B' and resid 225 through 228 Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 173 removed outlier: 4.055A pdb=" N LYS B 171 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AA7, first strand: chain 'B' and resid 522 through 526 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.770A pdb=" N GLY H 33 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 130 through 134 removed outlier: 4.043A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 130 through 134 removed outlier: 4.043A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.835A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LYS L 112 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL L 13 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.835A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LYS L 112 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL L 13 " --> pdb=" O LYS L 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.682A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 150 through 154 Processing sheet with id=AB8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.299A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N SER N 120 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL N 12 " --> pdb=" O SER N 120 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LYS N 99 " --> pdb=" O ARG N 33 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG N 33 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N MET N 34 " --> pdb=" O ALA N 50 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.299A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N SER N 120 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL N 12 " --> pdb=" O SER N 120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.921A pdb=" N VAL R 395 " --> pdb=" O ILE R 358 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'R' and resid 473 through 474 423 hydrogen bonds defined for protein. 1116 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: 3.12 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2864 1.35 - 1.48: 2471 1.48 - 1.61: 3844 1.61 - 1.74: 0 1.74 - 1.87: 47 Bond restraints: 9226 Sorted by residual: bond pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 1.808 1.875 -0.067 3.30e-02 9.18e+02 4.09e+00 bond pdb=" CB VAL N 48 " pdb=" CG2 VAL N 48 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.68e+00 bond pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 1.808 1.768 0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" C1 GLC A 1 " pdb=" O1 GLC A 1 " ideal model delta sigma weight residual 1.389 1.409 -0.020 2.00e-02 2.50e+03 9.63e-01 bond pdb=" C ILE B 133 " pdb=" N PRO B 134 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.00e-01 ... (remaining 9221 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.69: 274 106.69 - 113.52: 4944 113.52 - 120.34: 3306 120.34 - 127.16: 3900 127.16 - 133.98: 103 Bond angle restraints: 12527 Sorted by residual: angle pdb=" N CYS R 432 " pdb=" CA CYS R 432 " pdb=" C CYS R 432 " ideal model delta sigma weight residual 107.88 119.63 -11.75 1.41e+00 5.03e-01 6.95e+01 angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 127.67 -13.27 2.30e+00 1.89e-01 3.33e+01 angle pdb=" C GLY R 431 " pdb=" N CYS R 432 " pdb=" CA CYS R 432 " ideal model delta sigma weight residual 122.45 118.44 4.01 1.78e+00 3.16e-01 5.07e+00 angle pdb=" N GLU B 23 " pdb=" CA GLU B 23 " pdb=" CB GLU B 23 " ideal model delta sigma weight residual 110.16 113.37 -3.21 1.48e+00 4.57e-01 4.70e+00 angle pdb=" C GLU B 173 " pdb=" N ASN B 174 " pdb=" CA ASN B 174 " ideal model delta sigma weight residual 121.54 125.58 -4.04 1.91e+00 2.74e-01 4.47e+00 ... (remaining 12522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4970 17.94 - 35.87: 423 35.87 - 53.81: 73 53.81 - 71.75: 14 71.75 - 89.68: 11 Dihedral angle restraints: 5491 sinusoidal: 2164 harmonic: 3327 Sorted by residual: dihedral pdb=" CA GLU H 158 " pdb=" C GLU H 158 " pdb=" N PRO H 159 " pdb=" CA PRO H 159 " ideal model delta harmonic sigma weight residual 180.00 144.49 35.51 0 5.00e+00 4.00e-02 5.04e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual 93.00 34.17 58.83 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CB CYS H 150 " pdb=" SG CYS H 150 " pdb=" SG CYS H 206 " pdb=" CB CYS H 206 " ideal model delta sinusoidal sigma weight residual 93.00 140.09 -47.09 1 1.00e+01 1.00e-02 3.06e+01 ... (remaining 5488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1180 0.061 - 0.121: 177 0.121 - 0.182: 8 0.182 - 0.242: 0 0.242 - 0.303: 2 Chirality restraints: 1367 Sorted by residual: chirality pdb=" C1 GLC A 2 " pdb=" O4 GLC A 1 " pdb=" C2 GLC A 2 " pdb=" O5 GLC A 2 " both_signs ideal model delta sigma weight residual False 2.40 2.32 0.08 2.00e-02 2.50e+03 1.72e+01 chirality pdb=" C1 GLC A 1 " pdb=" C2 GLC A 1 " pdb=" O1 GLC A 1 " pdb=" O5 GLC A 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.34 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA CYS R 432 " pdb=" N CYS R 432 " pdb=" C CYS R 432 " pdb=" CB CYS R 432 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1364 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 158 " 0.076 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO H 159 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 383 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO R 384 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO R 384 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 384 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 123 " 0.050 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO B 124 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.042 5.00e-02 4.00e+02 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 200 2.69 - 3.24: 8625 3.24 - 3.80: 14199 3.80 - 4.35: 18927 4.35 - 4.90: 31721 Nonbonded interactions: 73672 Sorted by model distance: nonbonded pdb=" OD1 ASP R 442 " pdb=" OH TYR R 451 " model vdw 2.138 2.440 nonbonded pdb=" O MET H 110 " pdb=" OH TYR L 42 " model vdw 2.140 2.440 nonbonded pdb=" ND2 ASN H 207 " pdb=" OD1 ASP H 218 " model vdw 2.145 2.520 nonbonded pdb=" OE1 GLN L 27 " pdb=" OG1 THR N 118 " model vdw 2.204 2.440 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.208 2.440 ... (remaining 73667 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 group one per residue 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: 0.850 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: 3.110 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.890 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9226 Z= 0.204 Angle : 0.575 13.271 12527 Z= 0.302 Chirality : 0.043 0.303 1367 Planarity : 0.005 0.117 1604 Dihedral : 13.839 89.685 3344 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.21 % Allowed : 0.21 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.47 (0.25), residues: 1118 helix: 0.60 (0.33), residues: 261 sheet: 0.60 (0.27), residues: 346 loop : 0.11 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 56 HIS 0.004 0.001 HIS H 35 PHE 0.020 0.002 PHE B 259 TYR 0.015 0.001 TYR R 505 ARG 0.003 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.028 Fit side-chains REVERT: B 405 HIS cc_start: 0.8620 (t-90) cc_final: 0.8062 (t-170) REVERT: B 485 LEU cc_start: 0.8913 (tp) cc_final: 0.8315 (tp) REVERT: H 6 GLU cc_start: 0.7247 (mp0) cc_final: 0.6941 (mp0) REVERT: H 153 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8255 (mmtp) outliers start: 2 outliers final: 0 residues processed: 143 average time/residue: 0.2053 time to fit residues: 41.2690 Evaluate side-chains 111 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 204 HIS L 143 ASN ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9226 Z= 0.232 Angle : 0.556 14.592 12527 Z= 0.290 Chirality : 0.042 0.166 1367 Planarity : 0.005 0.101 1604 Dihedral : 4.405 33.811 1277 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.45 % Allowed : 6.63 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1118 helix: 1.16 (0.32), residues: 264 sheet: 0.67 (0.27), residues: 343 loop : 0.09 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 PHE 0.027 0.002 PHE B 510 TYR 0.036 0.001 TYR R 505 ARG 0.005 0.000 ARG L 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.058 Fit side-chains REVERT: B 405 HIS cc_start: 0.8638 (t-90) cc_final: 0.8111 (t-170) outliers start: 14 outliers final: 12 residues processed: 135 average time/residue: 0.2047 time to fit residues: 39.2468 Evaluate side-chains 133 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 218 ASP Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain R residue 392 PHE Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 28 optimal weight: 20.0000 chunk 101 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 204 HIS ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9226 Z= 0.162 Angle : 0.513 13.319 12527 Z= 0.267 Chirality : 0.041 0.154 1367 Planarity : 0.004 0.090 1604 Dihedral : 4.215 31.843 1277 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.35 % Allowed : 10.66 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.81 (0.25), residues: 1118 helix: 1.29 (0.32), residues: 264 sheet: 0.66 (0.27), residues: 358 loop : 0.15 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 PHE 0.023 0.001 PHE B 510 TYR 0.024 0.001 TYR R 505 ARG 0.003 0.000 ARG L 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 1.038 Fit side-chains REVERT: B 405 HIS cc_start: 0.8617 (t-90) cc_final: 0.8190 (t-170) REVERT: B 532 PHE cc_start: 0.7459 (m-80) cc_final: 0.6732 (m-80) REVERT: H 219 LYS cc_start: 0.7449 (tppt) cc_final: 0.7111 (tppt) outliers start: 13 outliers final: 9 residues processed: 140 average time/residue: 0.2034 time to fit residues: 40.5304 Evaluate side-chains 130 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 0.0370 chunk 108 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 125 ASN B 204 HIS L 32 ASN ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9226 Z= 0.219 Angle : 0.526 11.524 12527 Z= 0.274 Chirality : 0.041 0.135 1367 Planarity : 0.004 0.079 1604 Dihedral : 4.214 30.039 1277 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.86 % Allowed : 12.42 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1118 helix: 1.53 (0.33), residues: 257 sheet: 0.70 (0.27), residues: 353 loop : 0.05 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 47 HIS 0.003 0.001 HIS H 35 PHE 0.018 0.002 PHE B 532 TYR 0.020 0.001 TYR R 505 ARG 0.002 0.000 ARG L 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.040 Fit side-chains REVERT: B 405 HIS cc_start: 0.8651 (t-90) cc_final: 0.8233 (t-170) REVERT: H 219 LYS cc_start: 0.7643 (tppt) cc_final: 0.7441 (tppt) REVERT: L 69 THR cc_start: 0.7992 (t) cc_final: 0.7717 (p) REVERT: L 87 GLU cc_start: 0.7984 (pp20) cc_final: 0.7352 (pp20) outliers start: 18 outliers final: 13 residues processed: 139 average time/residue: 0.1893 time to fit residues: 37.6986 Evaluate side-chains 133 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 120 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 218 ASP Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 125 ASN B 324 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 174 HIS L 95 HIS ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 493 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 9226 Z= 0.514 Angle : 0.694 15.907 12527 Z= 0.363 Chirality : 0.046 0.189 1367 Planarity : 0.005 0.064 1604 Dihedral : 4.975 33.034 1277 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.80 % Allowed : 14.49 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.28 (0.25), residues: 1118 helix: 1.17 (0.32), residues: 259 sheet: 0.49 (0.27), residues: 338 loop : -0.46 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 47 HIS 0.003 0.001 HIS N 125 PHE 0.019 0.002 PHE B 259 TYR 0.030 0.003 TYR L 97 ARG 0.003 0.001 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 0.992 Fit side-chains REVERT: B 532 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7419 (m-10) REVERT: L 69 THR cc_start: 0.8019 (t) cc_final: 0.7816 (p) REVERT: L 87 GLU cc_start: 0.7967 (pp20) cc_final: 0.7335 (pp20) outliers start: 27 outliers final: 19 residues processed: 145 average time/residue: 0.1968 time to fit residues: 40.5081 Evaluate side-chains 136 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 218 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 432 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 204 HIS B 283 ASN ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 493 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9226 Z= 0.196 Angle : 0.562 15.254 12527 Z= 0.291 Chirality : 0.042 0.194 1367 Planarity : 0.004 0.062 1604 Dihedral : 4.551 31.392 1277 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.69 % Allowed : 16.77 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.42 (0.25), residues: 1118 helix: 1.33 (0.32), residues: 265 sheet: 0.35 (0.26), residues: 356 loop : -0.25 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 47 HIS 0.013 0.001 HIS L 95 PHE 0.013 0.001 PHE B 532 TYR 0.019 0.001 TYR L 97 ARG 0.002 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 0.961 Fit side-chains REVERT: B 291 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7143 (mm) REVERT: B 532 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7255 (m-80) REVERT: L 69 THR cc_start: 0.7916 (t) cc_final: 0.7666 (p) REVERT: L 87 GLU cc_start: 0.7975 (pp20) cc_final: 0.7371 (pp20) outliers start: 26 outliers final: 20 residues processed: 136 average time/residue: 0.1942 time to fit residues: 38.1887 Evaluate side-chains 139 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 chunk 107 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9226 Z= 0.212 Angle : 0.557 14.512 12527 Z= 0.288 Chirality : 0.042 0.153 1367 Planarity : 0.004 0.049 1604 Dihedral : 4.410 31.409 1277 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.69 % Allowed : 17.08 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.46 (0.25), residues: 1118 helix: 1.41 (0.32), residues: 265 sheet: 0.34 (0.26), residues: 355 loop : -0.23 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.001 PHE B 532 TYR 0.020 0.001 TYR B 100 ARG 0.002 0.000 ARG R 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 0.957 Fit side-chains REVERT: B 291 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7164 (mm) REVERT: B 532 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: L 69 THR cc_start: 0.7907 (t) cc_final: 0.7640 (p) REVERT: L 87 GLU cc_start: 0.7968 (pp20) cc_final: 0.7381 (pp20) outliers start: 26 outliers final: 20 residues processed: 142 average time/residue: 0.1811 time to fit residues: 36.8709 Evaluate side-chains 145 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9226 Z= 0.182 Angle : 0.554 15.510 12527 Z= 0.283 Chirality : 0.041 0.194 1367 Planarity : 0.004 0.052 1604 Dihedral : 4.250 30.792 1277 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.80 % Allowed : 17.49 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.51 (0.25), residues: 1118 helix: 1.47 (0.32), residues: 267 sheet: 0.33 (0.26), residues: 357 loop : -0.18 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 PHE 0.011 0.001 PHE B 532 TYR 0.020 0.001 TYR B 100 ARG 0.002 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: B 291 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7056 (mm) REVERT: B 331 MET cc_start: 0.8357 (mtm) cc_final: 0.8051 (mtm) REVERT: B 532 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7259 (m-80) REVERT: L 87 GLU cc_start: 0.7984 (pp20) cc_final: 0.7390 (pp20) REVERT: N 48 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7719 (m) outliers start: 27 outliers final: 14 residues processed: 145 average time/residue: 0.1991 time to fit residues: 42.1803 Evaluate side-chains 138 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 461 LEU Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 chunk 60 optimal weight: 0.0570 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.0060 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.4914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9226 Z= 0.152 Angle : 0.550 17.512 12527 Z= 0.280 Chirality : 0.041 0.228 1367 Planarity : 0.004 0.047 1604 Dihedral : 4.078 30.302 1277 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.17 % Allowed : 18.63 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.58 (0.25), residues: 1118 helix: 1.48 (0.32), residues: 272 sheet: 0.45 (0.27), residues: 350 loop : -0.19 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 47 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE B 532 TYR 0.020 0.001 TYR B 100 ARG 0.001 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.935 Fit side-chains REVERT: B 291 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6960 (mm) REVERT: B 331 MET cc_start: 0.8349 (mtm) cc_final: 0.8134 (mtm) REVERT: B 532 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: L 87 GLU cc_start: 0.7966 (pp20) cc_final: 0.7419 (pp20) outliers start: 21 outliers final: 13 residues processed: 140 average time/residue: 0.1843 time to fit residues: 37.1571 Evaluate side-chains 140 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 532 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 461 LEU Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 88 optimal weight: 0.0570 chunk 9 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9226 Z= 0.199 Angle : 0.575 17.025 12527 Z= 0.292 Chirality : 0.042 0.223 1367 Planarity : 0.004 0.049 1604 Dihedral : 4.164 30.384 1277 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.07 % Allowed : 19.05 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.59 (0.25), residues: 1118 helix: 1.55 (0.33), residues: 267 sheet: 0.50 (0.27), residues: 346 loop : -0.23 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 PHE 0.026 0.001 PHE B 259 TYR 0.019 0.001 TYR B 100 ARG 0.002 0.000 ARG R 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.991 Fit side-chains REVERT: B 291 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6902 (mm) REVERT: L 87 GLU cc_start: 0.7996 (pp20) cc_final: 0.7395 (pp20) REVERT: N 48 VAL cc_start: 0.7955 (OUTLIER) cc_final: 0.7652 (m) outliers start: 20 outliers final: 16 residues processed: 137 average time/residue: 0.2183 time to fit residues: 42.9142 Evaluate side-chains 142 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 94 CYS Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 461 LEU Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.0670 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 0.0370 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.176989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.144527 restraints weight = 11066.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136741 restraints weight = 13858.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134731 restraints weight = 14818.674| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 9226 Z= 0.277 Angle : 0.916 59.200 12527 Z= 0.528 Chirality : 0.043 0.422 1367 Planarity : 0.004 0.045 1604 Dihedral : 4.238 30.287 1277 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.07 % Allowed : 19.46 % Favored : 78.47 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.59 (0.25), residues: 1118 helix: 1.55 (0.33), residues: 267 sheet: 0.50 (0.27), residues: 346 loop : -0.23 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 PHE 0.025 0.001 PHE B 259 TYR 0.018 0.001 TYR B 100 ARG 0.002 0.000 ARG R 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1993.16 seconds wall clock time: 37 minutes 51.10 seconds (2271.10 seconds total)