Starting phenix.real_space_refine on Tue Sep 24 01:12:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9w_24263/09_2024/7n9w_24263.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9w_24263/09_2024/7n9w_24263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9w_24263/09_2024/7n9w_24263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9w_24263/09_2024/7n9w_24263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9w_24263/09_2024/7n9w_24263.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9w_24263/09_2024/7n9w_24263.cif" } resolution = 4.16 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= 0.003 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4317 2.51 5 N 1087 2.21 5 O 1117 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6561 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3277 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 19, 'TRANS': 425} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3284 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 425} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Time building chain proxies: 4.40, per 1000 atoms: 0.67 Number of scatterers: 6561 At special positions: 0 Unit cell: (92.224, 111.088, 75.456, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1117 8.00 N 1087 7.00 C 4317 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1552 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 1 sheets defined 73.1% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 36 through 46 removed outlier: 3.529A pdb=" N LEU A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 70 Processing helix chain 'A' and resid 74 through 100 removed outlier: 4.028A pdb=" N LEU A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.599A pdb=" N GLY A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 116 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 removed outlier: 3.697A pdb=" N LEU A 128 " --> pdb=" O TRP A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 148 through 167 removed outlier: 4.213A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 178 through 190 removed outlier: 5.821A pdb=" N ALA A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 203 removed outlier: 3.779A pdb=" N ILE A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.136A pdb=" N PHE A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE A 232 " --> pdb=" O MET A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 282 removed outlier: 4.199A pdb=" N TYR A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 4.078A pdb=" N ASP A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.508A pdb=" N TRP A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.638A pdb=" N THR A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 363 through 378 removed outlier: 3.686A pdb=" N LEU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 4.487A pdb=" N TYR A 382 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.649A pdb=" N ILE A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 392 " --> pdb=" O THR A 388 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.664A pdb=" N MET A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 439 removed outlier: 3.956A pdb=" N PHE A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 removed outlier: 4.949A pdb=" N LEU A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 455 " --> pdb=" O ARG A 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 29 through 70 removed outlier: 3.592A pdb=" N LEU B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLY B 47 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ALA B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 101 removed outlier: 4.029A pdb=" N LEU B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 89 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS B 99 " --> pdb=" O PHE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 removed outlier: 4.228A pdb=" N GLY B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 126 removed outlier: 3.685A pdb=" N ARG B 126 " --> pdb=" O ARG B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 126' Processing helix chain 'B' and resid 127 through 138 removed outlier: 3.964A pdb=" N PHE B 133 " --> pdb=" O PRO B 129 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 137 " --> pdb=" O PHE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 165 removed outlier: 4.172A pdb=" N THR B 151 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 removed outlier: 3.788A pdb=" N HIS B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.608A pdb=" N ALA B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 202 removed outlier: 3.569A pdb=" N PHE B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 233 removed outlier: 3.800A pdb=" N ILE B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET B 228 " --> pdb=" O MET B 224 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 284 removed outlier: 3.871A pdb=" N LEU B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) Proline residue: B 267 - end of helix removed outlier: 3.969A pdb=" N ASP B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 308 removed outlier: 4.322A pdb=" N LEU B 293 " --> pdb=" O THR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 347 removed outlier: 3.794A pdb=" N VAL B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 342 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 379 removed outlier: 3.986A pdb=" N ALA B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 395 removed outlier: 3.695A pdb=" N GLY B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 405 through 416 removed outlier: 4.057A pdb=" N LEU B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 430 removed outlier: 3.835A pdb=" N MET B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 443 through 459 removed outlier: 3.679A pdb=" N LYS B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 211 366 hydrogen bonds defined for protein. 1083 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: 1.75 Time building geometry restraints manager: 1.86 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: 1942 1.34 - 1.46: 1085 1.46 - 1.57: 3603 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6704 Sorted by residual: bond pdb=" C THR A 31 " pdb=" N PRO A 32 " ideal model delta sigma weight residual 1.334 1.380 -0.047 8.40e-03 1.42e+04 3.12e+01 bond pdb=" C THR B 31 " pdb=" N PRO B 32 " ideal model delta sigma weight residual 1.335 1.383 -0.048 1.30e-02 5.92e+03 1.38e+01 bond pdb=" N ILE B 200 " pdb=" CA ILE B 200 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.26e-02 6.30e+03 9.52e+00 bond pdb=" N ILE B 197 " pdb=" CA ILE B 197 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.21e-02 6.83e+03 7.95e+00 bond pdb=" N ILE B 201 " pdb=" CA ILE B 201 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.30e-02 5.92e+03 7.30e+00 ... (remaining 6699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 8678 2.22 - 4.45: 363 4.45 - 6.67: 48 6.67 - 8.89: 20 8.89 - 11.12: 5 Bond angle restraints: 9114 Sorted by residual: angle pdb=" N VAL B 162 " pdb=" CA VAL B 162 " pdb=" C VAL B 162 " ideal model delta sigma weight residual 112.29 105.57 6.72 9.40e-01 1.13e+00 5.11e+01 angle pdb=" N ILE B 322 " pdb=" CA ILE B 322 " pdb=" C ILE B 322 " ideal model delta sigma weight residual 112.83 106.50 6.33 9.90e-01 1.02e+00 4.09e+01 angle pdb=" C LYS B 30 " pdb=" N THR B 31 " pdb=" CA THR B 31 " ideal model delta sigma weight residual 120.58 126.56 -5.98 1.32e+00 5.74e-01 2.05e+01 angle pdb=" N VAL B 236 " pdb=" CA VAL B 236 " pdb=" C VAL B 236 " ideal model delta sigma weight residual 110.21 105.36 4.85 1.13e+00 7.83e-01 1.84e+01 angle pdb=" C GLY B 108 " pdb=" N ILE B 109 " pdb=" CA ILE B 109 " ideal model delta sigma weight residual 122.13 129.90 -7.77 1.85e+00 2.92e-01 1.76e+01 ... (remaining 9109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 3422 17.07 - 34.13: 354 34.13 - 51.20: 85 51.20 - 68.27: 7 68.27 - 85.34: 3 Dihedral angle restraints: 3871 sinusoidal: 1413 harmonic: 2458 Sorted by residual: dihedral pdb=" CA ALA A 237 " pdb=" C ALA A 237 " pdb=" N LEU A 238 " pdb=" CA LEU A 238 " ideal model delta harmonic sigma weight residual -180.00 -152.21 -27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA VAL B 162 " pdb=" C VAL B 162 " pdb=" N LEU B 163 " pdb=" CA LEU B 163 " ideal model delta harmonic sigma weight residual 180.00 155.96 24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA PRO A 359 " pdb=" C PRO A 359 " pdb=" N MET A 360 " pdb=" CA MET A 360 " ideal model delta harmonic sigma weight residual 180.00 157.24 22.76 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 3868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 899 0.077 - 0.153: 165 0.153 - 0.230: 15 0.230 - 0.307: 2 0.307 - 0.384: 1 Chirality restraints: 1082 Sorted by residual: chirality pdb=" CB ILE A 320 " pdb=" CA ILE A 320 " pdb=" CG1 ILE A 320 " pdb=" CG2 ILE A 320 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA ILE B 197 " pdb=" N ILE B 197 " pdb=" C ILE B 197 " pdb=" CB ILE B 197 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ILE B 201 " pdb=" N ILE B 201 " pdb=" C ILE B 201 " pdb=" CB ILE B 201 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1079 not shown) Planarity restraints: 1143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 149 " -0.049 5.00e-02 4.00e+02 7.43e-02 8.83e+00 pdb=" N PRO A 150 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 406 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C LEU B 406 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU B 406 " 0.018 2.00e-02 2.50e+03 pdb=" N THR B 407 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 423 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO B 424 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 424 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 424 " 0.039 5.00e-02 4.00e+02 ... (remaining 1140 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1621 2.79 - 3.32: 6249 3.32 - 3.84: 10814 3.84 - 4.37: 12137 4.37 - 4.90: 20550 Nonbonded interactions: 51371 Sorted by model distance: nonbonded pdb=" OG SER A 107 " pdb=" O GLY A 354 " model vdw 2.258 3.040 nonbonded pdb=" O LEU A 435 " pdb=" OG1 THR A 439 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR A 94 " pdb=" OG SER A 350 " model vdw 2.296 3.040 nonbonded pdb=" O PRO A 206 " pdb=" OH TYR A 210 " model vdw 2.326 3.040 nonbonded pdb=" OE2 GLU A 103 " pdb=" OE2 GLU A 111 " model vdw 2.328 3.040 ... (remaining 51366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 17 through 29 and (name N or name CA or name C or name O \ or name CB )) or resid 30 through 461)) selection = (chain 'B' and (resid 17 through 206 or (resid 207 through 208 and (name N or na \ me CA or name C or name O or name CB )) or resid 209 through 461)) } 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.060 Find NCS groups from input model: 0.250 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.005 0.060 6704 Z= 0.339 Angle : 1.079 11.119 9114 Z= 0.598 Chirality : 0.060 0.384 1082 Planarity : 0.007 0.074 1143 Dihedral : 14.637 85.335 2319 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.66 % Favored : 93.23 % Rotamer: Outliers : 1.40 % Allowed : 10.08 % Favored : 88.53 % 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: -5.14 (0.21), residues: 886 helix: -3.34 (0.14), residues: 574 sheet: None (None), residues: 0 loop : -3.21 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 291 HIS 0.003 0.001 HIS B 70 PHE 0.027 0.002 PHE B 357 TYR 0.011 0.002 TYR A 100 ARG 0.003 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 201 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7153 (tt) REVERT: A 55 LYS cc_start: 0.8757 (mttt) cc_final: 0.8446 (mtmt) REVERT: A 148 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 202 GLU cc_start: 0.6820 (tp30) cc_final: 0.6455 (tp30) REVERT: A 235 GLU cc_start: 0.8001 (tt0) cc_final: 0.7729 (tt0) REVERT: A 246 ASP cc_start: 0.6429 (t0) cc_final: 0.6062 (t0) REVERT: A 277 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7975 (tm-30) REVERT: A 278 ASP cc_start: 0.8257 (p0) cc_final: 0.8013 (p0) REVERT: A 279 LEU cc_start: 0.8845 (mp) cc_final: 0.8332 (tt) REVERT: A 294 MET cc_start: 0.8943 (tmm) cc_final: 0.8691 (tmm) REVERT: A 329 SER cc_start: 0.7621 (m) cc_final: 0.6904 (t) REVERT: A 360 MET cc_start: 0.8399 (mtp) cc_final: 0.7468 (mtp) REVERT: A 418 ASN cc_start: 0.9254 (m-40) cc_final: 0.8768 (m-40) REVERT: A 434 LEU cc_start: 0.8637 (tt) cc_final: 0.8416 (tt) REVERT: A 456 GLN cc_start: 0.8739 (tp40) cc_final: 0.8166 (tm-30) REVERT: B 35 ILE cc_start: 0.9261 (tt) cc_final: 0.8993 (tp) REVERT: B 55 LYS cc_start: 0.7375 (tmtt) cc_final: 0.7089 (tmtt) REVERT: B 59 TRP cc_start: 0.8608 (t60) cc_final: 0.8118 (t60) REVERT: B 161 MET cc_start: 0.7420 (ttt) cc_final: 0.7139 (ttm) REVERT: B 208 PHE cc_start: 0.6564 (m-80) cc_final: 0.6152 (m-10) REVERT: B 210 TYR cc_start: 0.7105 (m-10) cc_final: 0.6875 (m-10) REVERT: B 276 MET cc_start: 0.8975 (tpp) cc_final: 0.8643 (tpt) REVERT: B 277 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7259 (tm-30) REVERT: B 278 ASP cc_start: 0.8125 (t0) cc_final: 0.7789 (p0) REVERT: B 291 TRP cc_start: 0.7849 (t-100) cc_final: 0.7561 (t-100) REVERT: B 332 MET cc_start: 0.7899 (tpp) cc_final: 0.7406 (tpp) REVERT: B 342 ILE cc_start: 0.9037 (tt) cc_final: 0.8826 (tp) REVERT: B 382 TYR cc_start: 0.8635 (m-80) cc_final: 0.8242 (m-80) REVERT: B 410 ILE cc_start: 0.8471 (mm) cc_final: 0.8116 (mm) outliers start: 9 outliers final: 3 residues processed: 206 average time/residue: 0.1739 time to fit residues: 47.5411 Evaluate side-chains 165 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 161 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 30.0000 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6704 Z= 0.242 Angle : 0.702 8.365 9114 Z= 0.357 Chirality : 0.043 0.198 1082 Planarity : 0.006 0.052 1143 Dihedral : 5.745 28.404 938 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.21 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % 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: -3.39 (0.25), residues: 886 helix: -1.91 (0.19), residues: 570 sheet: None (None), residues: 0 loop : -2.66 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 59 HIS 0.004 0.001 HIS A 284 PHE 0.015 0.001 PHE B 357 TYR 0.011 0.001 TYR A 210 ARG 0.003 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8896 (m) cc_final: 0.8636 (t) REVERT: A 91 MET cc_start: 0.8186 (mpp) cc_final: 0.7841 (mpp) REVERT: A 148 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7749 (tm-30) REVERT: A 202 GLU cc_start: 0.7072 (tp30) cc_final: 0.6718 (tp30) REVERT: A 219 PHE cc_start: 0.8265 (m-80) cc_final: 0.7994 (m-80) REVERT: A 246 ASP cc_start: 0.6331 (t0) cc_final: 0.5897 (t0) REVERT: A 279 LEU cc_start: 0.8880 (mp) cc_final: 0.8450 (tt) REVERT: A 294 MET cc_start: 0.9025 (tmm) cc_final: 0.8598 (tmm) REVERT: A 342 ILE cc_start: 0.8628 (tp) cc_final: 0.8362 (tp) REVERT: A 360 MET cc_start: 0.8396 (mtp) cc_final: 0.7926 (mtp) REVERT: A 382 TYR cc_start: 0.7721 (m-80) cc_final: 0.7460 (m-80) REVERT: A 391 ILE cc_start: 0.9261 (mm) cc_final: 0.9033 (mm) REVERT: A 456 GLN cc_start: 0.8713 (tp40) cc_final: 0.8162 (tm-30) REVERT: B 55 LYS cc_start: 0.7453 (tmtt) cc_final: 0.7139 (tmtt) REVERT: B 59 TRP cc_start: 0.8715 (t60) cc_final: 0.8105 (t60) REVERT: B 61 GLN cc_start: 0.8620 (mt0) cc_final: 0.7795 (mp10) REVERT: B 65 MET cc_start: 0.8305 (tmm) cc_final: 0.7639 (tmm) REVERT: B 136 LEU cc_start: 0.9028 (mt) cc_final: 0.8789 (mt) REVERT: B 191 ASN cc_start: 0.8214 (t0) cc_final: 0.7849 (t0) REVERT: B 197 ILE cc_start: 0.8474 (mt) cc_final: 0.8217 (mt) REVERT: B 276 MET cc_start: 0.8974 (tpp) cc_final: 0.8701 (tpt) REVERT: B 277 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7335 (tm-30) REVERT: B 278 ASP cc_start: 0.8298 (t0) cc_final: 0.7960 (p0) REVERT: B 293 LEU cc_start: 0.8762 (mm) cc_final: 0.8525 (mm) REVERT: B 438 PHE cc_start: 0.8005 (t80) cc_final: 0.7793 (t80) REVERT: B 457 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7381 (mm-30) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1521 time to fit residues: 41.2747 Evaluate side-chains 154 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 40.0000 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.0060 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6704 Z= 0.187 Angle : 0.657 7.588 9114 Z= 0.329 Chirality : 0.042 0.167 1082 Planarity : 0.005 0.052 1143 Dihedral : 5.247 24.871 938 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.16 % Allowed : 5.27 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.27), residues: 886 helix: -1.30 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -2.33 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 59 HIS 0.003 0.001 HIS A 284 PHE 0.017 0.001 PHE B 357 TYR 0.008 0.001 TYR A 210 ARG 0.003 0.000 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8515 (mttt) cc_final: 0.8293 (mttt) REVERT: A 143 MET cc_start: 0.7304 (mtm) cc_final: 0.7101 (mtt) REVERT: A 148 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7726 (tm-30) REVERT: A 202 GLU cc_start: 0.7138 (tp30) cc_final: 0.6759 (tp30) REVERT: A 219 PHE cc_start: 0.8203 (m-80) cc_final: 0.7939 (m-80) REVERT: A 224 MET cc_start: 0.8270 (tpt) cc_final: 0.7879 (tpp) REVERT: A 228 MET cc_start: 0.7848 (mtt) cc_final: 0.7456 (mtp) REVERT: A 279 LEU cc_start: 0.8873 (mp) cc_final: 0.8460 (tt) REVERT: A 329 SER cc_start: 0.7853 (m) cc_final: 0.7272 (t) REVERT: A 342 ILE cc_start: 0.8604 (tp) cc_final: 0.8353 (tp) REVERT: A 360 MET cc_start: 0.8350 (mtp) cc_final: 0.8103 (mtp) REVERT: A 456 GLN cc_start: 0.8706 (tp40) cc_final: 0.8113 (tm-30) REVERT: B 55 LYS cc_start: 0.7481 (tmtt) cc_final: 0.7173 (tmtt) REVERT: B 59 TRP cc_start: 0.8669 (t60) cc_final: 0.8179 (t60) REVERT: B 61 GLN cc_start: 0.8636 (mt0) cc_final: 0.7871 (mp10) REVERT: B 124 TRP cc_start: 0.7713 (p-90) cc_final: 0.7121 (p-90) REVERT: B 132 PHE cc_start: 0.8463 (t80) cc_final: 0.8244 (t80) REVERT: B 136 LEU cc_start: 0.9039 (mt) cc_final: 0.8813 (mt) REVERT: B 191 ASN cc_start: 0.8097 (t0) cc_final: 0.7850 (t0) REVERT: B 197 ILE cc_start: 0.8426 (mt) cc_final: 0.8206 (mt) REVERT: B 270 ASN cc_start: 0.9192 (m-40) cc_final: 0.8341 (m110) REVERT: B 278 ASP cc_start: 0.8285 (t0) cc_final: 0.7980 (p0) REVERT: B 282 ARG cc_start: 0.7104 (tpp80) cc_final: 0.6854 (ttm-80) REVERT: B 330 MET cc_start: 0.7667 (mpp) cc_final: 0.6913 (tpt) REVERT: B 413 LEU cc_start: 0.8418 (mm) cc_final: 0.8194 (mt) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.1566 time to fit residues: 43.6132 Evaluate side-chains 168 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6704 Z= 0.184 Angle : 0.654 7.195 9114 Z= 0.327 Chirality : 0.042 0.135 1082 Planarity : 0.005 0.045 1143 Dihedral : 5.021 20.051 938 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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: -2.15 (0.27), residues: 886 helix: -0.95 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -2.18 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 59 HIS 0.003 0.001 HIS A 284 PHE 0.018 0.001 PHE A 307 TYR 0.018 0.001 TYR B 210 ARG 0.004 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 0.723 Fit side-chains REVERT: A 88 VAL cc_start: 0.9003 (t) cc_final: 0.8664 (t) REVERT: A 91 MET cc_start: 0.8235 (mpp) cc_final: 0.7944 (mpp) REVERT: A 143 MET cc_start: 0.7327 (mtm) cc_final: 0.7083 (mtt) REVERT: A 148 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7727 (tm-30) REVERT: A 219 PHE cc_start: 0.8193 (m-80) cc_final: 0.7845 (m-80) REVERT: A 329 SER cc_start: 0.7813 (m) cc_final: 0.7248 (t) REVERT: A 342 ILE cc_start: 0.8586 (tp) cc_final: 0.8299 (tp) REVERT: A 360 MET cc_start: 0.8320 (mtp) cc_final: 0.7848 (mtm) REVERT: A 456 GLN cc_start: 0.8678 (tp40) cc_final: 0.8076 (tm-30) REVERT: B 55 LYS cc_start: 0.7445 (tmtt) cc_final: 0.7130 (tmtt) REVERT: B 59 TRP cc_start: 0.8599 (t60) cc_final: 0.8167 (t60) REVERT: B 61 GLN cc_start: 0.8696 (mt0) cc_final: 0.7861 (mp10) REVERT: B 119 GLN cc_start: 0.8396 (mp10) cc_final: 0.8121 (mp10) REVERT: B 124 TRP cc_start: 0.7712 (p-90) cc_final: 0.7106 (p-90) REVERT: B 132 PHE cc_start: 0.8423 (t80) cc_final: 0.8196 (t80) REVERT: B 136 LEU cc_start: 0.9021 (mt) cc_final: 0.8811 (mt) REVERT: B 197 ILE cc_start: 0.8451 (mt) cc_final: 0.8218 (mt) REVERT: B 270 ASN cc_start: 0.9173 (m-40) cc_final: 0.8305 (m110) REVERT: B 278 ASP cc_start: 0.8279 (t0) cc_final: 0.7927 (p0) REVERT: B 332 MET cc_start: 0.7883 (tpp) cc_final: 0.7368 (tpp) REVERT: B 457 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7293 (mm-30) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1542 time to fit residues: 42.8387 Evaluate side-chains 165 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN A 157 ASN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6704 Z= 0.301 Angle : 0.714 8.349 9114 Z= 0.354 Chirality : 0.044 0.150 1082 Planarity : 0.005 0.046 1143 Dihedral : 5.182 20.910 938 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % 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: -1.86 (0.28), residues: 886 helix: -0.68 (0.22), residues: 576 sheet: None (None), residues: 0 loop : -2.17 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 59 HIS 0.004 0.001 HIS A 284 PHE 0.018 0.001 PHE B 357 TYR 0.016 0.002 TYR B 210 ARG 0.005 0.001 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7729 (tm-30) REVERT: A 202 GLU cc_start: 0.7075 (tp30) cc_final: 0.6818 (tp30) REVERT: A 228 MET cc_start: 0.7913 (mtt) cc_final: 0.7498 (mtp) REVERT: A 279 LEU cc_start: 0.8952 (mt) cc_final: 0.8682 (tt) REVERT: A 294 MET cc_start: 0.8946 (tmm) cc_final: 0.8671 (tpp) REVERT: A 329 SER cc_start: 0.7937 (m) cc_final: 0.7355 (t) REVERT: A 342 ILE cc_start: 0.8638 (tp) cc_final: 0.8329 (tp) REVERT: A 360 MET cc_start: 0.8426 (mtp) cc_final: 0.8025 (mtp) REVERT: A 456 GLN cc_start: 0.8720 (tp40) cc_final: 0.8113 (tm-30) REVERT: B 38 MET cc_start: 0.8547 (mmt) cc_final: 0.8210 (mmt) REVERT: B 55 LYS cc_start: 0.7527 (tmtt) cc_final: 0.7199 (tmtt) REVERT: B 59 TRP cc_start: 0.8902 (t60) cc_final: 0.8566 (t60) REVERT: B 136 LEU cc_start: 0.9033 (mt) cc_final: 0.8806 (mt) REVERT: B 157 ASN cc_start: 0.8842 (m-40) cc_final: 0.8622 (m-40) REVERT: B 171 ASP cc_start: 0.8164 (p0) cc_final: 0.7920 (p0) REVERT: B 228 MET cc_start: 0.7587 (mmt) cc_final: 0.7129 (tpp) REVERT: B 270 ASN cc_start: 0.9266 (m-40) cc_final: 0.8463 (m110) REVERT: B 278 ASP cc_start: 0.8338 (t0) cc_final: 0.8008 (p0) REVERT: B 282 ARG cc_start: 0.7199 (tpp80) cc_final: 0.6954 (ttm-80) REVERT: B 332 MET cc_start: 0.7927 (tpp) cc_final: 0.7427 (tpp) REVERT: B 346 LEU cc_start: 0.8280 (tp) cc_final: 0.7973 (tp) REVERT: B 413 LEU cc_start: 0.8485 (mt) cc_final: 0.8279 (mt) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1524 time to fit residues: 38.8270 Evaluate side-chains 157 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 50.0000 chunk 82 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6704 Z= 0.350 Angle : 0.756 9.641 9114 Z= 0.376 Chirality : 0.046 0.151 1082 Planarity : 0.005 0.047 1143 Dihedral : 5.347 21.632 938 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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: -1.87 (0.27), residues: 886 helix: -0.66 (0.22), residues: 580 sheet: None (None), residues: 0 loop : -2.24 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 59 HIS 0.004 0.001 HIS A 284 PHE 0.019 0.002 PHE B 357 TYR 0.015 0.002 TYR B 210 ARG 0.005 0.001 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.985 Fit side-chains REVERT: A 29 ASP cc_start: 0.6669 (m-30) cc_final: 0.6465 (m-30) REVERT: A 83 PHE cc_start: 0.8002 (t80) cc_final: 0.7779 (t80) REVERT: A 88 VAL cc_start: 0.8982 (t) cc_final: 0.8681 (t) REVERT: A 148 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7966 (tm-30) REVERT: A 202 GLU cc_start: 0.7093 (tp30) cc_final: 0.6848 (tp30) REVERT: A 246 ASP cc_start: 0.6321 (t0) cc_final: 0.6119 (t0) REVERT: A 279 LEU cc_start: 0.8874 (mt) cc_final: 0.8605 (tt) REVERT: A 294 MET cc_start: 0.8868 (tmm) cc_final: 0.8551 (tpp) REVERT: A 342 ILE cc_start: 0.8678 (tp) cc_final: 0.8285 (tp) REVERT: A 360 MET cc_start: 0.8402 (mtp) cc_final: 0.7997 (mtp) REVERT: A 456 GLN cc_start: 0.8752 (tp40) cc_final: 0.8101 (tm-30) REVERT: B 55 LYS cc_start: 0.7573 (tmtt) cc_final: 0.7259 (tmtt) REVERT: B 59 TRP cc_start: 0.9010 (t60) cc_final: 0.8436 (t60) REVERT: B 197 ILE cc_start: 0.8441 (mt) cc_final: 0.8211 (mt) REVERT: B 210 TYR cc_start: 0.7412 (m-10) cc_final: 0.7008 (m-10) REVERT: B 228 MET cc_start: 0.7623 (mmt) cc_final: 0.7173 (tpp) REVERT: B 246 ASP cc_start: 0.7809 (t70) cc_final: 0.7028 (m-30) REVERT: B 270 ASN cc_start: 0.9268 (m-40) cc_final: 0.8441 (m110) REVERT: B 278 ASP cc_start: 0.8422 (t0) cc_final: 0.8011 (p0) REVERT: B 282 ARG cc_start: 0.7265 (tpp80) cc_final: 0.7022 (ttm-80) REVERT: B 291 TRP cc_start: 0.8201 (t-100) cc_final: 0.7713 (t-100) REVERT: B 346 LEU cc_start: 0.8263 (tp) cc_final: 0.7967 (tp) REVERT: B 349 SER cc_start: 0.9297 (m) cc_final: 0.8946 (t) REVERT: B 356 ILE cc_start: 0.9154 (tt) cc_final: 0.8926 (tt) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1590 time to fit residues: 41.4534 Evaluate side-chains 154 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN B 62 ASN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6704 Z= 0.204 Angle : 0.679 7.740 9114 Z= 0.337 Chirality : 0.043 0.166 1082 Planarity : 0.005 0.043 1143 Dihedral : 4.989 18.813 938 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: -1.53 (0.28), residues: 886 helix: -0.47 (0.22), residues: 580 sheet: None (None), residues: 0 loop : -1.92 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 59 HIS 0.003 0.001 HIS A 284 PHE 0.020 0.001 PHE B 357 TYR 0.014 0.001 TYR B 255 ARG 0.008 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.6597 (m-30) cc_final: 0.6377 (m-30) REVERT: A 38 MET cc_start: 0.8215 (tpp) cc_final: 0.7921 (mmp) REVERT: A 83 PHE cc_start: 0.7937 (t80) cc_final: 0.7691 (t80) REVERT: A 88 VAL cc_start: 0.9066 (t) cc_final: 0.8760 (t) REVERT: A 91 MET cc_start: 0.8130 (mpp) cc_final: 0.7863 (mpp) REVERT: A 148 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7690 (tm-30) REVERT: A 202 GLU cc_start: 0.6999 (tp30) cc_final: 0.6732 (tp30) REVERT: A 219 PHE cc_start: 0.8311 (m-80) cc_final: 0.8087 (m-80) REVERT: A 224 MET cc_start: 0.8277 (tpt) cc_final: 0.8037 (tpp) REVERT: A 228 MET cc_start: 0.7462 (mtt) cc_final: 0.7166 (mtp) REVERT: A 246 ASP cc_start: 0.6262 (t0) cc_final: 0.6000 (t0) REVERT: A 279 LEU cc_start: 0.8841 (mt) cc_final: 0.8584 (tt) REVERT: A 294 MET cc_start: 0.8897 (tmm) cc_final: 0.8592 (tpp) REVERT: A 329 SER cc_start: 0.7939 (m) cc_final: 0.7382 (t) REVERT: A 456 GLN cc_start: 0.8697 (tp40) cc_final: 0.8125 (tm-30) REVERT: B 38 MET cc_start: 0.8501 (mmt) cc_final: 0.8224 (mmt) REVERT: B 55 LYS cc_start: 0.7538 (tmtt) cc_final: 0.7130 (tmtt) REVERT: B 59 TRP cc_start: 0.8942 (t60) cc_final: 0.8646 (t60) REVERT: B 120 ARG cc_start: 0.8307 (mtp85) cc_final: 0.8084 (tpp80) REVERT: B 197 ILE cc_start: 0.8622 (mt) cc_final: 0.8344 (mt) REVERT: B 210 TYR cc_start: 0.7316 (m-10) cc_final: 0.7099 (m-10) REVERT: B 228 MET cc_start: 0.7609 (mmt) cc_final: 0.7181 (tpp) REVERT: B 270 ASN cc_start: 0.9246 (m-40) cc_final: 0.8346 (m110) REVERT: B 278 ASP cc_start: 0.8241 (t0) cc_final: 0.8002 (p0) REVERT: B 282 ARG cc_start: 0.7226 (tpp80) cc_final: 0.6894 (ttm-80) REVERT: B 291 TRP cc_start: 0.8152 (t-100) cc_final: 0.7668 (t-100) REVERT: B 346 LEU cc_start: 0.8032 (tp) cc_final: 0.7726 (tp) REVERT: B 418 ASN cc_start: 0.8920 (m-40) cc_final: 0.8331 (t0) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1546 time to fit residues: 40.1915 Evaluate side-chains 160 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 0.0270 chunk 74 optimal weight: 0.6980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6704 Z= 0.205 Angle : 0.677 7.696 9114 Z= 0.334 Chirality : 0.043 0.176 1082 Planarity : 0.005 0.044 1143 Dihedral : 4.874 18.904 938 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: -1.39 (0.28), residues: 886 helix: -0.42 (0.22), residues: 586 sheet: None (None), residues: 0 loop : -1.74 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 59 HIS 0.003 0.001 HIS A 284 PHE 0.020 0.001 PHE B 357 TYR 0.013 0.001 TYR B 210 ARG 0.006 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.6580 (m-30) cc_final: 0.6374 (m-30) REVERT: A 38 MET cc_start: 0.8306 (tpp) cc_final: 0.8016 (mmp) REVERT: A 83 PHE cc_start: 0.7961 (t80) cc_final: 0.7712 (t80) REVERT: A 88 VAL cc_start: 0.8972 (t) cc_final: 0.8656 (t) REVERT: A 91 MET cc_start: 0.8188 (mpp) cc_final: 0.7923 (mpp) REVERT: A 133 PHE cc_start: 0.7875 (t80) cc_final: 0.6745 (m-80) REVERT: A 148 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 202 GLU cc_start: 0.6897 (tp30) cc_final: 0.6690 (tp30) REVERT: A 219 PHE cc_start: 0.8317 (m-80) cc_final: 0.8114 (m-80) REVERT: A 224 MET cc_start: 0.8355 (tpt) cc_final: 0.8094 (tpp) REVERT: A 228 MET cc_start: 0.7700 (mtt) cc_final: 0.7321 (mtp) REVERT: A 246 ASP cc_start: 0.6253 (t0) cc_final: 0.6004 (t0) REVERT: A 279 LEU cc_start: 0.8824 (mt) cc_final: 0.8603 (tt) REVERT: A 294 MET cc_start: 0.8842 (tmm) cc_final: 0.8492 (tpp) REVERT: A 329 SER cc_start: 0.7983 (m) cc_final: 0.7409 (t) REVERT: A 330 MET cc_start: 0.8816 (tpt) cc_final: 0.8480 (tpt) REVERT: A 360 MET cc_start: 0.8348 (mtp) cc_final: 0.7506 (mtp) REVERT: A 373 MET cc_start: 0.8826 (ptm) cc_final: 0.8159 (ptm) REVERT: A 456 GLN cc_start: 0.8683 (tp40) cc_final: 0.8119 (tm-30) REVERT: B 55 LYS cc_start: 0.7545 (tmtt) cc_final: 0.7178 (tmtt) REVERT: B 59 TRP cc_start: 0.8957 (t60) cc_final: 0.8718 (t60) REVERT: B 120 ARG cc_start: 0.8373 (mtp85) cc_final: 0.8104 (tpp80) REVERT: B 197 ILE cc_start: 0.8608 (mt) cc_final: 0.8347 (mt) REVERT: B 210 TYR cc_start: 0.7291 (m-10) cc_final: 0.7087 (m-10) REVERT: B 228 MET cc_start: 0.7601 (mmt) cc_final: 0.7176 (tpp) REVERT: B 270 ASN cc_start: 0.9265 (m-40) cc_final: 0.8432 (m110) REVERT: B 278 ASP cc_start: 0.8292 (t0) cc_final: 0.8028 (p0) REVERT: B 282 ARG cc_start: 0.7185 (tpp80) cc_final: 0.6879 (ttm-80) REVERT: B 291 TRP cc_start: 0.8151 (t-100) cc_final: 0.7669 (t-100) REVERT: B 346 LEU cc_start: 0.8120 (tp) cc_final: 0.7725 (tp) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1508 time to fit residues: 39.9626 Evaluate side-chains 162 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6704 Z= 0.204 Angle : 0.684 7.868 9114 Z= 0.339 Chirality : 0.044 0.184 1082 Planarity : 0.005 0.047 1143 Dihedral : 4.865 18.978 938 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -1.34 (0.28), residues: 886 helix: -0.41 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -1.69 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 59 HIS 0.003 0.001 HIS A 284 PHE 0.022 0.001 PHE A 307 TYR 0.012 0.001 TYR B 210 ARG 0.006 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.6681 (m-30) cc_final: 0.6472 (m-30) REVERT: A 38 MET cc_start: 0.8336 (tpp) cc_final: 0.8054 (mmp) REVERT: A 83 PHE cc_start: 0.7938 (t80) cc_final: 0.7683 (t80) REVERT: A 88 VAL cc_start: 0.8966 (t) cc_final: 0.8645 (t) REVERT: A 91 MET cc_start: 0.8190 (mpp) cc_final: 0.7901 (mpp) REVERT: A 133 PHE cc_start: 0.7919 (t80) cc_final: 0.6698 (m-80) REVERT: A 148 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7699 (tm-30) REVERT: A 202 GLU cc_start: 0.6898 (tp30) cc_final: 0.6631 (tp30) REVERT: A 219 PHE cc_start: 0.8305 (m-80) cc_final: 0.8095 (m-80) REVERT: A 224 MET cc_start: 0.8300 (tpt) cc_final: 0.8042 (tpp) REVERT: A 228 MET cc_start: 0.7621 (mtt) cc_final: 0.7265 (mtp) REVERT: A 246 ASP cc_start: 0.6284 (t0) cc_final: 0.6023 (t0) REVERT: A 279 LEU cc_start: 0.8822 (mt) cc_final: 0.8604 (tt) REVERT: A 294 MET cc_start: 0.8830 (tmm) cc_final: 0.8470 (tpp) REVERT: A 329 SER cc_start: 0.7975 (m) cc_final: 0.7415 (t) REVERT: A 330 MET cc_start: 0.8772 (tpt) cc_final: 0.8480 (tpt) REVERT: A 360 MET cc_start: 0.8329 (mtp) cc_final: 0.7883 (mtp) REVERT: A 373 MET cc_start: 0.8835 (ptm) cc_final: 0.8170 (ptm) REVERT: A 456 GLN cc_start: 0.8667 (tp40) cc_final: 0.8111 (tm-30) REVERT: B 38 MET cc_start: 0.8204 (mmt) cc_final: 0.7915 (mmt) REVERT: B 55 LYS cc_start: 0.7517 (tmtt) cc_final: 0.7110 (tmtt) REVERT: B 118 ASP cc_start: 0.7016 (m-30) cc_final: 0.6768 (m-30) REVERT: B 120 ARG cc_start: 0.8332 (mtp85) cc_final: 0.8076 (tpp80) REVERT: B 197 ILE cc_start: 0.8545 (mt) cc_final: 0.8286 (mt) REVERT: B 210 TYR cc_start: 0.7260 (m-10) cc_final: 0.7004 (m-10) REVERT: B 228 MET cc_start: 0.7612 (mmt) cc_final: 0.7190 (tpp) REVERT: B 270 ASN cc_start: 0.9249 (m-40) cc_final: 0.8383 (m110) REVERT: B 278 ASP cc_start: 0.8281 (t0) cc_final: 0.8042 (p0) REVERT: B 282 ARG cc_start: 0.7168 (tpp80) cc_final: 0.6832 (ttm-80) REVERT: B 291 TRP cc_start: 0.8148 (t-100) cc_final: 0.7691 (t-100) REVERT: B 346 LEU cc_start: 0.8063 (tp) cc_final: 0.7631 (tp) REVERT: B 416 THR cc_start: 0.9034 (m) cc_final: 0.8777 (p) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1468 time to fit residues: 37.6553 Evaluate side-chains 159 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.4980 chunk 39 optimal weight: 0.0670 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6704 Z= 0.182 Angle : 0.672 7.869 9114 Z= 0.332 Chirality : 0.043 0.176 1082 Planarity : 0.005 0.047 1143 Dihedral : 4.751 19.273 938 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -1.34 (0.28), residues: 886 helix: -0.40 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -1.72 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 59 HIS 0.003 0.001 HIS A 284 PHE 0.036 0.001 PHE B 357 TYR 0.010 0.001 TYR B 255 ARG 0.006 0.000 ARG B 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8253 (tpp) cc_final: 0.7995 (mmp) REVERT: A 83 PHE cc_start: 0.7912 (t80) cc_final: 0.7702 (t80) REVERT: A 88 VAL cc_start: 0.8941 (t) cc_final: 0.8630 (t) REVERT: A 91 MET cc_start: 0.8202 (mpp) cc_final: 0.7893 (mpp) REVERT: A 133 PHE cc_start: 0.7809 (t80) cc_final: 0.6693 (m-10) REVERT: A 148 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7698 (tm-30) REVERT: A 202 GLU cc_start: 0.6754 (tp30) cc_final: 0.6475 (tp30) REVERT: A 219 PHE cc_start: 0.8250 (m-80) cc_final: 0.8027 (m-80) REVERT: A 224 MET cc_start: 0.8290 (tpt) cc_final: 0.8077 (tpp) REVERT: A 228 MET cc_start: 0.7560 (mtt) cc_final: 0.7227 (mtp) REVERT: A 279 LEU cc_start: 0.8834 (mt) cc_final: 0.8601 (tt) REVERT: A 294 MET cc_start: 0.8826 (tmm) cc_final: 0.8466 (tpp) REVERT: A 329 SER cc_start: 0.7957 (m) cc_final: 0.7356 (t) REVERT: A 330 MET cc_start: 0.8805 (tpt) cc_final: 0.8482 (tpt) REVERT: A 360 MET cc_start: 0.8388 (mtp) cc_final: 0.7931 (mtp) REVERT: A 373 MET cc_start: 0.8768 (ptm) cc_final: 0.8003 (ptm) REVERT: A 456 GLN cc_start: 0.8635 (tp40) cc_final: 0.8096 (tm-30) REVERT: B 38 MET cc_start: 0.8168 (mmt) cc_final: 0.7767 (mmt) REVERT: B 55 LYS cc_start: 0.7458 (tmtt) cc_final: 0.7039 (tmtt) REVERT: B 118 ASP cc_start: 0.7022 (m-30) cc_final: 0.6770 (m-30) REVERT: B 197 ILE cc_start: 0.8543 (mt) cc_final: 0.8292 (mt) REVERT: B 202 GLU cc_start: 0.7109 (tp30) cc_final: 0.6766 (tp30) REVERT: B 228 MET cc_start: 0.7418 (mmt) cc_final: 0.7029 (tpp) REVERT: B 270 ASN cc_start: 0.9228 (m-40) cc_final: 0.8404 (m110) REVERT: B 278 ASP cc_start: 0.8266 (t0) cc_final: 0.8038 (p0) REVERT: B 282 ARG cc_start: 0.7132 (tpp80) cc_final: 0.6771 (ttm-80) REVERT: B 291 TRP cc_start: 0.8127 (t-100) cc_final: 0.7678 (t-100) REVERT: B 413 LEU cc_start: 0.8253 (mm) cc_final: 0.8014 (mt) REVERT: B 416 THR cc_start: 0.9204 (m) cc_final: 0.8976 (p) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1624 time to fit residues: 41.9201 Evaluate side-chains 164 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.147328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.122049 restraints weight = 11063.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125245 restraints weight = 7210.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.127532 restraints weight = 5379.048| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6704 Z= 0.205 Angle : 0.679 7.786 9114 Z= 0.336 Chirality : 0.044 0.179 1082 Planarity : 0.005 0.048 1143 Dihedral : 4.788 19.325 938 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -1.21 (0.29), residues: 886 helix: -0.30 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.65 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 59 HIS 0.003 0.001 HIS A 284 PHE 0.034 0.001 PHE B 357 TYR 0.011 0.001 TYR B 210 ARG 0.006 0.000 ARG B 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1527.23 seconds wall clock time: 27 minutes 38.23 seconds (1658.23 seconds total)