Starting phenix.real_space_refine on Wed Feb 14 03:36:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/02_2024/7zbu_14591_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/02_2024/7zbu_14591.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/02_2024/7zbu_14591_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/02_2024/7zbu_14591_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/02_2024/7zbu_14591_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/02_2024/7zbu_14591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/02_2024/7zbu_14591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/02_2024/7zbu_14591_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/02_2024/7zbu_14591_updated.pdb" } resolution = 4.31 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= 0.016 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 34 5.16 5 C 5429 2.51 5 N 1406 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 89": "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: 8529 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5206 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 625} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1708 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 211} Chain breaks: 1 Chain: "L" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1460 Classifications: {'peptide': 192} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 179} Chain breaks: 2 Chain: "A" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 155 Unusual residues: {'3Q9': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 4.86, per 1000 atoms: 0.57 Number of scatterers: 8529 At special positions: 0 Unit cell: (84.7, 114.4, 171.6, 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 34 16.00 O 1660 8.00 N 1406 7.00 C 5429 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 156 " - pdb=" SG CYS H 212 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " 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 NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 17 " " NAG A1304 " - " ASN A 122 " " NAG A1305 " - " ASN A 165 " " NAG A1306 " - " ASN A 282 " " NAG A1307 " - " ASN A 61 " " NAG A1308 " - " ASN A 149 " Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.6 seconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 21 sheets defined 5.5% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.997A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.528A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 202 through 205 No H-bonds generated for 'chain 'H' and resid 202 through 205' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 124 through 129 Processing sheet with id= A, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.148A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.024A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.866A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 243 through 246 removed outlier: 6.847A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 311 through 313 Processing sheet with id= F, first strand: chain 'A' and resid 325 through 328 removed outlier: 8.873A pdb=" N ILE A 326 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN A 540 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ARG A 328 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN A 542 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 354 through 358 Processing sheet with id= H, first strand: chain 'A' and resid 361 through 363 removed outlier: 3.611A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 363 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= J, first strand: chain 'A' and resid 643 through 645 Processing sheet with id= K, first strand: chain 'A' and resid 691 through 695 removed outlier: 6.586A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.517A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 123 through 125 removed outlier: 5.721A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 99 through 106 removed outlier: 3.732A pdb=" N SER H 106 " --> pdb=" O GLN H 109 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN H 109 " --> pdb=" O SER H 106 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 136 through 140 removed outlier: 3.750A pdb=" N GLY H 155 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 167 through 170 Processing sheet with id= Q, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= R, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.660A pdb=" N ARG L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'L' and resid 86 through 91 removed outlier: 5.981A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 116 through 120 Processing sheet with id= U, first strand: chain 'L' and resid 146 through 149 removed outlier: 3.624A pdb=" N LYS L 147 " --> pdb=" O THR L 199 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 660 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2685 1.34 - 1.47: 2300 1.47 - 1.59: 3714 1.59 - 1.72: 1 1.72 - 1.84: 40 Bond restraints: 8740 Sorted by residual: bond pdb=" CAB 3Q9 A1309 " pdb=" CBB 3Q9 A1309 " ideal model delta sigma weight residual 1.533 1.306 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" CAC 3Q9 A1309 " pdb=" CBC 3Q9 A1309 " ideal model delta sigma weight residual 1.531 1.307 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C4D 3Q9 A1309 " pdb=" CHA 3Q9 A1309 " ideal model delta sigma weight residual 1.564 1.377 0.187 2.00e-02 2.50e+03 8.75e+01 bond pdb=" C4C 3Q9 A1309 " pdb=" CHD 3Q9 A1309 " ideal model delta sigma weight residual 1.547 1.371 0.176 2.00e-02 2.50e+03 7.72e+01 bond pdb=" C1B 3Q9 A1309 " pdb=" CHB 3Q9 A1309 " ideal model delta sigma weight residual 1.544 1.369 0.175 2.00e-02 2.50e+03 7.66e+01 ... (remaining 8735 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.59: 257 106.59 - 113.44: 4664 113.44 - 120.28: 2969 120.28 - 127.13: 3906 127.13 - 133.98: 101 Bond angle restraints: 11897 Sorted by residual: angle pdb=" C3C 3Q9 A1309 " pdb=" CAC 3Q9 A1309 " pdb=" CBC 3Q9 A1309 " ideal model delta sigma weight residual 109.52 128.53 -19.01 3.00e+00 1.11e-01 4.01e+01 angle pdb=" C3B 3Q9 A1309 " pdb=" CAB 3Q9 A1309 " pdb=" CBB 3Q9 A1309 " ideal model delta sigma weight residual 109.54 127.89 -18.35 3.00e+00 1.11e-01 3.74e+01 angle pdb=" C1B 3Q9 A1309 " pdb=" CHB 3Q9 A1309 " pdb=" C4A 3Q9 A1309 " ideal model delta sigma weight residual 109.46 127.68 -18.22 3.00e+00 1.11e-01 3.69e+01 angle pdb=" CA PRO L 143 " pdb=" N PRO L 143 " pdb=" CD PRO L 143 " ideal model delta sigma weight residual 111.50 104.60 6.90 1.40e+00 5.10e-01 2.43e+01 angle pdb=" C1A 3Q9 A1309 " pdb=" CHA 3Q9 A1309 " pdb=" C4D 3Q9 A1309 " ideal model delta sigma weight residual 109.55 124.21 -14.66 3.00e+00 1.11e-01 2.39e+01 ... (remaining 11892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4850 17.97 - 35.93: 329 35.93 - 53.90: 54 53.90 - 71.86: 19 71.86 - 89.83: 13 Dihedral angle restraints: 5265 sinusoidal: 2148 harmonic: 3117 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 144.27 -51.27 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -122.45 36.45 1 1.00e+01 1.00e-02 1.88e+01 dihedral pdb=" CA CYS A 336 " pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " ideal model delta sinusoidal sigma weight residual -73.00 -4.67 -68.33 1 2.00e+01 2.50e-03 1.51e+01 ... (remaining 5262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 1329 0.139 - 0.278: 5 0.278 - 0.417: 2 0.417 - 0.556: 0 0.556 - 0.694: 1 Chirality restraints: 1337 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CB ILE A 584 " pdb=" CA ILE A 584 " pdb=" CG1 ILE A 584 " pdb=" CG2 ILE A 584 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 1334 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D 3Q9 A1309 " -0.019 2.00e-02 2.50e+03 2.61e-02 1.53e+01 pdb=" C2D 3Q9 A1309 " -0.008 2.00e-02 2.50e+03 pdb=" C3D 3Q9 A1309 " -0.010 2.00e-02 2.50e+03 pdb=" C4D 3Q9 A1309 " -0.020 2.00e-02 2.50e+03 pdb=" CAD 3Q9 A1309 " -0.003 2.00e-02 2.50e+03 pdb=" CHA 3Q9 A1309 " 0.048 2.00e-02 2.50e+03 pdb=" CHD 3Q9 A1309 " 0.034 2.00e-02 2.50e+03 pdb=" CMD 3Q9 A1309 " 0.016 2.00e-02 2.50e+03 pdb=" N_D 3Q9 A1309 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR L 142 " 0.057 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO L 143 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO L 143 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO L 143 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1B 3Q9 A1309 " 0.004 2.00e-02 2.50e+03 2.14e-02 1.03e+01 pdb=" C2B 3Q9 A1309 " -0.001 2.00e-02 2.50e+03 pdb=" C3B 3Q9 A1309 " 0.003 2.00e-02 2.50e+03 pdb=" C4B 3Q9 A1309 " -0.007 2.00e-02 2.50e+03 pdb=" CAB 3Q9 A1309 " 0.037 2.00e-02 2.50e+03 pdb=" CHB 3Q9 A1309 " 0.027 2.00e-02 2.50e+03 pdb=" CMB 3Q9 A1309 " -0.038 2.00e-02 2.50e+03 pdb=" N_B 3Q9 A1309 " -0.006 2.00e-02 2.50e+03 pdb=" O_B 3Q9 A1309 " -0.020 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 106 2.64 - 3.20: 7519 3.20 - 3.77: 12398 3.77 - 4.33: 17312 4.33 - 4.90: 28249 Nonbonded interactions: 65584 Sorted by model distance: nonbonded pdb=" O PRO A 85 " pdb=" OH TYR A 269 " model vdw 2.071 2.440 nonbonded pdb=" NH1 ARG H 38 " pdb=" OD1 ASP H 90 " model vdw 2.115 2.520 nonbonded pdb=" OD1 ASP A 53 " pdb=" N LEU A 54 " model vdw 2.131 2.520 nonbonded pdb=" NH1 ARG A 457 " pdb=" O SER A 459 " model vdw 2.179 2.520 nonbonded pdb=" OE2 GLU A 298 " pdb=" NH2 ARG A 319 " model vdw 2.205 2.520 ... (remaining 65579 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: 2.190 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: 8.000 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 25.800 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 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 : 0.008 0.227 8740 Z= 0.543 Angle : 0.819 19.007 11897 Z= 0.394 Chirality : 0.053 0.694 1337 Planarity : 0.005 0.083 1518 Dihedral : 13.041 89.829 3235 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.21 % Allowed : 0.00 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1058 helix: -0.27 (0.77), residues: 46 sheet: 0.16 (0.26), residues: 367 loop : -0.82 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 436 HIS 0.004 0.001 HIS A 49 PHE 0.019 0.002 PHE A 559 TYR 0.017 0.001 TYR A 269 ARG 0.008 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 372 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7908 (p) cc_final: 0.7236 (t) REVERT: A 38 TYR cc_start: 0.7429 (m-80) cc_final: 0.6132 (m-80) REVERT: A 55 PHE cc_start: 0.7144 (m-80) cc_final: 0.6767 (m-10) REVERT: A 63 THR cc_start: 0.7567 (p) cc_final: 0.7082 (t) REVERT: A 91 TYR cc_start: 0.7082 (t80) cc_final: 0.6405 (t80) REVERT: A 204 TYR cc_start: 0.6104 (m-80) cc_final: 0.5104 (m-80) REVERT: A 319 ARG cc_start: 0.5539 (mtm-85) cc_final: 0.4942 (ptp90) REVERT: A 321 GLN cc_start: 0.7491 (tt0) cc_final: 0.7097 (tt0) REVERT: A 329 PHE cc_start: 0.7158 (m-80) cc_final: 0.6938 (m-80) REVERT: A 338 PHE cc_start: 0.7954 (m-80) cc_final: 0.7512 (m-80) REVERT: A 355 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7837 (tpp80) REVERT: A 358 ILE cc_start: 0.8147 (mm) cc_final: 0.7728 (mm) REVERT: A 366 SER cc_start: 0.8769 (m) cc_final: 0.8342 (p) REVERT: A 433 VAL cc_start: 0.7830 (t) cc_final: 0.7450 (p) REVERT: A 453 TYR cc_start: 0.6769 (p90) cc_final: 0.6394 (p90) REVERT: A 461 LEU cc_start: 0.7969 (mm) cc_final: 0.7632 (mm) REVERT: A 468 ILE cc_start: 0.8677 (pt) cc_final: 0.8406 (mm) REVERT: A 532 ASN cc_start: 0.7866 (t0) cc_final: 0.7421 (t0) REVERT: A 542 ASN cc_start: 0.6710 (p0) cc_final: 0.6453 (p0) REVERT: A 546 LEU cc_start: 0.7543 (tt) cc_final: 0.7254 (tp) REVERT: A 556 ASN cc_start: 0.7859 (p0) cc_final: 0.7457 (p0) REVERT: A 563 GLN cc_start: 0.7033 (tt0) cc_final: 0.6819 (tt0) REVERT: A 564 GLN cc_start: 0.8111 (mm110) cc_final: 0.7660 (mp10) REVERT: A 574 ASP cc_start: 0.6875 (m-30) cc_final: 0.6641 (m-30) REVERT: A 582 LEU cc_start: 0.7738 (mt) cc_final: 0.6741 (mt) REVERT: A 584 ILE cc_start: 0.8130 (tt) cc_final: 0.7076 (tt) REVERT: A 692 ILE cc_start: 0.7415 (mt) cc_final: 0.6926 (mt) REVERT: H 36 TRP cc_start: 0.7888 (m100) cc_final: 0.7152 (m100) REVERT: H 38 ARG cc_start: 0.7118 (ptt180) cc_final: 0.6889 (ptp90) REVERT: H 67 ARG cc_start: 0.6692 (mtp180) cc_final: 0.6345 (mtp180) REVERT: H 125 VAL cc_start: 0.8809 (p) cc_final: 0.8437 (m) REVERT: H 138 PHE cc_start: 0.7692 (m-80) cc_final: 0.7445 (m-80) REVERT: H 166 VAL cc_start: 0.8833 (p) cc_final: 0.8433 (m) REVERT: H 186 LEU cc_start: 0.7023 (pp) cc_final: 0.6812 (pp) REVERT: H 188 SER cc_start: 0.8875 (m) cc_final: 0.8552 (p) REVERT: L 5 THR cc_start: 0.6583 (p) cc_final: 0.6295 (m) REVERT: L 38 GLN cc_start: 0.6444 (pt0) cc_final: 0.6206 (pt0) REVERT: L 50 TYR cc_start: 0.7253 (p90) cc_final: 0.6877 (p90) REVERT: L 55 ARG cc_start: 0.7006 (mtp85) cc_final: 0.6715 (ptm160) REVERT: L 72 PHE cc_start: 0.7282 (m-80) cc_final: 0.6302 (m-10) REVERT: L 128 LYS cc_start: 0.8592 (tptm) cc_final: 0.8065 (tptm) REVERT: L 175 TYR cc_start: 0.6853 (m-80) cc_final: 0.6619 (m-10) outliers start: 2 outliers final: 0 residues processed: 373 average time/residue: 0.2293 time to fit residues: 112.5781 Evaluate side-chains 324 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 54 optimal weight: 0.0870 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 137 ASN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 394 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 82 GLN L 38 GLN L 39 GLN L 90 GLN L 91 GLN ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8740 Z= 0.226 Angle : 0.668 7.722 11897 Z= 0.339 Chirality : 0.048 0.462 1337 Planarity : 0.005 0.045 1518 Dihedral : 7.412 79.440 1352 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.53 % Allowed : 2.57 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1058 helix: -0.38 (0.77), residues: 47 sheet: 0.49 (0.26), residues: 359 loop : -0.73 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 436 HIS 0.011 0.002 HIS A 207 PHE 0.028 0.002 PHE A 275 TYR 0.021 0.002 TYR A 365 ARG 0.006 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 353 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6851 (mtp85) cc_final: 0.6402 (mtp85) REVERT: A 38 TYR cc_start: 0.7771 (m-80) cc_final: 0.6944 (m-80) REVERT: A 53 ASP cc_start: 0.7443 (t0) cc_final: 0.6932 (t0) REVERT: A 55 PHE cc_start: 0.7076 (m-80) cc_final: 0.6663 (m-10) REVERT: A 63 THR cc_start: 0.7681 (p) cc_final: 0.6926 (t) REVERT: A 91 TYR cc_start: 0.7195 (t80) cc_final: 0.6324 (t80) REVERT: A 96 GLU cc_start: 0.5777 (mm-30) cc_final: 0.5556 (mm-30) REVERT: A 133 PHE cc_start: 0.5817 (m-80) cc_final: 0.5502 (m-80) REVERT: A 204 TYR cc_start: 0.5966 (m-80) cc_final: 0.4914 (m-80) REVERT: A 206 LYS cc_start: 0.8551 (tppt) cc_final: 0.7866 (tptp) REVERT: A 235 ILE cc_start: 0.7679 (mt) cc_final: 0.7455 (mt) REVERT: A 293 LEU cc_start: 0.8405 (tp) cc_final: 0.8019 (tp) REVERT: A 357 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7803 (mtp85) REVERT: A 366 SER cc_start: 0.8834 (m) cc_final: 0.8413 (p) REVERT: A 368 LEU cc_start: 0.8453 (mm) cc_final: 0.8207 (mt) REVERT: A 392 PHE cc_start: 0.7679 (m-80) cc_final: 0.7461 (m-10) REVERT: A 403 ARG cc_start: 0.7096 (ptm-80) cc_final: 0.6857 (ptm-80) REVERT: A 441 LEU cc_start: 0.8583 (pp) cc_final: 0.8358 (pt) REVERT: A 461 LEU cc_start: 0.7966 (mm) cc_final: 0.7458 (mm) REVERT: A 468 ILE cc_start: 0.8700 (pt) cc_final: 0.8382 (mm) REVERT: A 540 ASN cc_start: 0.7783 (m-40) cc_final: 0.7425 (m-40) REVERT: A 544 ASN cc_start: 0.7444 (m-40) cc_final: 0.7128 (m-40) REVERT: A 556 ASN cc_start: 0.7870 (p0) cc_final: 0.7616 (p0) REVERT: A 558 LYS cc_start: 0.6806 (ttmm) cc_final: 0.6384 (ttmm) REVERT: A 572 THR cc_start: 0.8242 (t) cc_final: 0.7810 (p) REVERT: A 574 ASP cc_start: 0.6991 (m-30) cc_final: 0.6789 (m-30) REVERT: H 38 ARG cc_start: 0.7771 (ptt180) cc_final: 0.6865 (ptt180) REVERT: H 100 ASP cc_start: 0.7720 (t0) cc_final: 0.7360 (t0) REVERT: H 125 VAL cc_start: 0.8900 (p) cc_final: 0.8525 (m) REVERT: H 166 VAL cc_start: 0.8825 (p) cc_final: 0.7767 (m) REVERT: H 186 LEU cc_start: 0.7545 (pp) cc_final: 0.7306 (pp) REVERT: H 188 SER cc_start: 0.8974 (m) cc_final: 0.8655 (p) REVERT: H 215 ASN cc_start: 0.6565 (m-40) cc_final: 0.5771 (m-40) REVERT: H 222 LYS cc_start: 0.7720 (tptp) cc_final: 0.7492 (tppt) REVERT: L 40 LYS cc_start: 0.8615 (ptpp) cc_final: 0.8298 (ptpp) REVERT: L 46 ARG cc_start: 0.8248 (ttp-170) cc_final: 0.7856 (ttp-170) REVERT: L 50 TYR cc_start: 0.7373 (p90) cc_final: 0.6731 (p90) REVERT: L 72 PHE cc_start: 0.7371 (m-80) cc_final: 0.6494 (m-80) REVERT: L 128 LYS cc_start: 0.8596 (tptm) cc_final: 0.8094 (tptm) REVERT: L 162 GLN cc_start: 0.8128 (tp-100) cc_final: 0.7885 (tp-100) outliers start: 5 outliers final: 0 residues processed: 355 average time/residue: 0.2279 time to fit residues: 106.6388 Evaluate side-chains 329 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 0.0870 chunk 97 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 87 ASN A 137 ASN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8740 Z= 0.249 Angle : 0.673 7.509 11897 Z= 0.345 Chirality : 0.048 0.433 1337 Planarity : 0.005 0.046 1518 Dihedral : 7.336 85.639 1352 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.21 % Allowed : 3.21 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1058 helix: -0.55 (0.75), residues: 46 sheet: 0.37 (0.26), residues: 346 loop : -0.74 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 119 HIS 0.008 0.001 HIS A 207 PHE 0.034 0.002 PHE A 275 TYR 0.019 0.002 TYR L 175 ARG 0.009 0.001 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 355 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.7529 (t) cc_final: 0.7296 (p) REVERT: A 37 TYR cc_start: 0.7367 (p90) cc_final: 0.6887 (p90) REVERT: A 38 TYR cc_start: 0.7930 (m-80) cc_final: 0.6173 (m-80) REVERT: A 55 PHE cc_start: 0.7216 (m-80) cc_final: 0.6942 (m-80) REVERT: A 196 ASN cc_start: 0.7685 (t0) cc_final: 0.7414 (t0) REVERT: A 204 TYR cc_start: 0.6253 (m-80) cc_final: 0.5327 (m-80) REVERT: A 206 LYS cc_start: 0.8610 (tppt) cc_final: 0.8007 (tmtt) REVERT: A 235 ILE cc_start: 0.7725 (mt) cc_final: 0.7505 (mt) REVERT: A 328 ARG cc_start: 0.7945 (mmt90) cc_final: 0.7674 (mmt90) REVERT: A 329 PHE cc_start: 0.7282 (m-10) cc_final: 0.7043 (m-80) REVERT: A 366 SER cc_start: 0.8811 (m) cc_final: 0.8515 (p) REVERT: A 400 PHE cc_start: 0.7110 (p90) cc_final: 0.6873 (p90) REVERT: A 429 PHE cc_start: 0.7641 (t80) cc_final: 0.7318 (t80) REVERT: A 436 TRP cc_start: 0.6667 (p90) cc_final: 0.5866 (p90) REVERT: A 438 SER cc_start: 0.7583 (m) cc_final: 0.4672 (m) REVERT: A 453 TYR cc_start: 0.6736 (p90) cc_final: 0.6258 (p90) REVERT: A 461 LEU cc_start: 0.7880 (mm) cc_final: 0.7632 (mm) REVERT: A 468 ILE cc_start: 0.8733 (pt) cc_final: 0.8384 (mm) REVERT: A 518 LEU cc_start: 0.7917 (mp) cc_final: 0.7708 (mt) REVERT: A 535 LYS cc_start: 0.7496 (mtpt) cc_final: 0.7055 (mtpt) REVERT: A 540 ASN cc_start: 0.7891 (m-40) cc_final: 0.7612 (m110) REVERT: A 544 ASN cc_start: 0.7552 (m-40) cc_final: 0.7177 (m-40) REVERT: A 556 ASN cc_start: 0.7970 (p0) cc_final: 0.7662 (p0) REVERT: A 572 THR cc_start: 0.8322 (t) cc_final: 0.8043 (p) REVERT: A 578 ASP cc_start: 0.8096 (p0) cc_final: 0.7704 (p0) REVERT: H 6 GLU cc_start: 0.7842 (mp0) cc_final: 0.7563 (mp0) REVERT: H 27 PHE cc_start: 0.7821 (p90) cc_final: 0.7187 (p90) REVERT: H 39 GLN cc_start: 0.7518 (tt0) cc_final: 0.7276 (tt0) REVERT: H 89 GLU cc_start: 0.7362 (pp20) cc_final: 0.6944 (tm-30) REVERT: H 98 LYS cc_start: 0.8216 (ptmm) cc_final: 0.7890 (ptmm) REVERT: H 100 ASP cc_start: 0.7782 (t0) cc_final: 0.7558 (t0) REVERT: H 125 VAL cc_start: 0.8857 (p) cc_final: 0.8494 (m) REVERT: H 138 PHE cc_start: 0.7924 (m-80) cc_final: 0.7541 (m-80) REVERT: H 166 VAL cc_start: 0.8841 (p) cc_final: 0.8350 (m) REVERT: H 188 SER cc_start: 0.9069 (m) cc_final: 0.8852 (p) REVERT: H 217 LYS cc_start: 0.8681 (mtpp) cc_final: 0.8452 (mtpp) REVERT: L 37 TYR cc_start: 0.6834 (m-80) cc_final: 0.6604 (m-80) REVERT: L 39 GLN cc_start: 0.7871 (tp40) cc_final: 0.7556 (tp40) REVERT: L 50 TYR cc_start: 0.7204 (p90) cc_final: 0.6691 (p90) REVERT: L 61 ASP cc_start: 0.6957 (t0) cc_final: 0.6673 (t0) REVERT: L 72 PHE cc_start: 0.7405 (m-80) cc_final: 0.6764 (m-80) REVERT: L 89 CYS cc_start: 0.3273 (p) cc_final: 0.2882 (p) REVERT: L 102 GLN cc_start: 0.6808 (tp40) cc_final: 0.6585 (tp40) REVERT: L 126 GLN cc_start: 0.8865 (tt0) cc_final: 0.8658 (tt0) REVERT: L 128 LYS cc_start: 0.8618 (tptm) cc_final: 0.8186 (tptm) REVERT: L 162 GLN cc_start: 0.8113 (tp-100) cc_final: 0.7814 (tp-100) REVERT: L 165 VAL cc_start: 0.8901 (t) cc_final: 0.8699 (p) REVERT: L 207 VAL cc_start: 0.7440 (p) cc_final: 0.6657 (p) outliers start: 2 outliers final: 0 residues processed: 356 average time/residue: 0.2218 time to fit residues: 104.8510 Evaluate side-chains 313 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 GLN L 90 GLN ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 8740 Z= 0.272 Angle : 0.691 9.314 11897 Z= 0.356 Chirality : 0.048 0.436 1337 Planarity : 0.005 0.094 1518 Dihedral : 7.517 87.516 1352 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.21 % Allowed : 2.78 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1058 helix: -0.79 (0.67), residues: 61 sheet: 0.36 (0.26), residues: 349 loop : -0.89 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 64 HIS 0.011 0.002 HIS A 207 PHE 0.021 0.002 PHE A 55 TYR 0.020 0.002 TYR L 175 ARG 0.006 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 349 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7392 (p90) cc_final: 0.7140 (p90) REVERT: A 153 MET cc_start: 0.7199 (ppp) cc_final: 0.6978 (ppp) REVERT: A 196 ASN cc_start: 0.7840 (t0) cc_final: 0.7563 (t0) REVERT: A 204 TYR cc_start: 0.6384 (m-80) cc_final: 0.5696 (m-80) REVERT: A 206 LYS cc_start: 0.8682 (tppt) cc_final: 0.8151 (tmtt) REVERT: A 235 ILE cc_start: 0.7860 (mt) cc_final: 0.7648 (mt) REVERT: A 357 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7470 (tmm-80) REVERT: A 366 SER cc_start: 0.8855 (m) cc_final: 0.8563 (p) REVERT: A 386 LYS cc_start: 0.7999 (mmtm) cc_final: 0.7180 (mmtm) REVERT: A 403 ARG cc_start: 0.7043 (ptm-80) cc_final: 0.6742 (ptm-80) REVERT: A 428 ASP cc_start: 0.7427 (t0) cc_final: 0.7175 (t0) REVERT: A 429 PHE cc_start: 0.7593 (t80) cc_final: 0.7271 (t80) REVERT: A 453 TYR cc_start: 0.6809 (p90) cc_final: 0.6399 (p90) REVERT: A 468 ILE cc_start: 0.8734 (pt) cc_final: 0.8347 (mm) REVERT: A 529 LYS cc_start: 0.8207 (tptp) cc_final: 0.7989 (tptp) REVERT: A 535 LYS cc_start: 0.7506 (mtpt) cc_final: 0.6128 (mtmt) REVERT: A 544 ASN cc_start: 0.7556 (m-40) cc_final: 0.7163 (m-40) REVERT: A 556 ASN cc_start: 0.8030 (p0) cc_final: 0.7793 (p0) REVERT: A 558 LYS cc_start: 0.7157 (ttmm) cc_final: 0.6600 (mtpp) REVERT: A 568 ASP cc_start: 0.8065 (p0) cc_final: 0.7813 (p0) REVERT: A 572 THR cc_start: 0.8187 (t) cc_final: 0.7969 (p) REVERT: H 6 GLU cc_start: 0.7816 (mp0) cc_final: 0.7515 (mp0) REVERT: H 27 PHE cc_start: 0.7878 (p90) cc_final: 0.7293 (p90) REVERT: H 89 GLU cc_start: 0.7368 (pp20) cc_final: 0.7059 (tm-30) REVERT: H 98 LYS cc_start: 0.8256 (ptmm) cc_final: 0.7879 (ptmm) REVERT: H 100 ASP cc_start: 0.7717 (t0) cc_final: 0.7427 (t0) REVERT: H 117 ASP cc_start: 0.7769 (p0) cc_final: 0.7417 (p0) REVERT: H 123 THR cc_start: 0.8440 (m) cc_final: 0.8040 (p) REVERT: H 125 VAL cc_start: 0.8819 (p) cc_final: 0.8447 (m) REVERT: H 138 PHE cc_start: 0.8054 (m-80) cc_final: 0.7665 (m-80) REVERT: H 159 LYS cc_start: 0.8123 (tptt) cc_final: 0.7485 (tptt) REVERT: H 187 GLN cc_start: 0.7364 (pt0) cc_final: 0.6424 (pt0) REVERT: H 215 ASN cc_start: 0.6760 (m-40) cc_final: 0.5908 (m-40) REVERT: H 217 LYS cc_start: 0.8698 (mtpp) cc_final: 0.8475 (mtpp) REVERT: H 222 LYS cc_start: 0.7834 (tptp) cc_final: 0.7527 (tppt) REVERT: H 226 LYS cc_start: 0.8306 (tptt) cc_final: 0.8013 (tppt) REVERT: L 39 GLN cc_start: 0.7916 (tp40) cc_final: 0.7435 (tp40) REVERT: L 40 LYS cc_start: 0.8691 (ptpp) cc_final: 0.8413 (ptpp) REVERT: L 46 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7950 (ttp-170) REVERT: L 50 TYR cc_start: 0.7207 (p90) cc_final: 0.6759 (p90) REVERT: L 61 ASP cc_start: 0.7205 (t0) cc_final: 0.6887 (t0) REVERT: L 72 PHE cc_start: 0.7387 (m-80) cc_final: 0.6776 (m-80) REVERT: L 126 GLN cc_start: 0.8994 (tt0) cc_final: 0.8623 (tt0) REVERT: L 128 LYS cc_start: 0.8665 (tptm) cc_final: 0.8188 (tptm) REVERT: L 160 ASN cc_start: 0.6385 (p0) cc_final: 0.6178 (p0) REVERT: L 162 GLN cc_start: 0.8027 (tp-100) cc_final: 0.7676 (tp-100) REVERT: L 207 VAL cc_start: 0.7742 (p) cc_final: 0.7428 (t) outliers start: 2 outliers final: 0 residues processed: 349 average time/residue: 0.2361 time to fit residues: 109.4064 Evaluate side-chains 308 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 90 GLN L 91 GLN ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8740 Z= 0.265 Angle : 0.691 11.158 11897 Z= 0.355 Chirality : 0.048 0.423 1337 Planarity : 0.006 0.102 1518 Dihedral : 7.474 80.383 1352 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.11 % Allowed : 2.25 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.25), residues: 1058 helix: -0.96 (0.63), residues: 61 sheet: 0.17 (0.26), residues: 364 loop : -1.01 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 436 HIS 0.008 0.001 HIS A 207 PHE 0.027 0.002 PHE A 400 TYR 0.025 0.002 TYR H 114 ARG 0.006 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 332 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7542 (p90) cc_final: 0.7140 (p90) REVERT: A 137 ASN cc_start: 0.8379 (t0) cc_final: 0.8115 (t0) REVERT: A 191 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6850 (mt-10) REVERT: A 196 ASN cc_start: 0.7924 (t0) cc_final: 0.7709 (t0) REVERT: A 204 TYR cc_start: 0.6801 (m-80) cc_final: 0.6060 (m-80) REVERT: A 206 LYS cc_start: 0.8613 (tppt) cc_final: 0.7493 (tptp) REVERT: A 216 LEU cc_start: 0.8541 (mt) cc_final: 0.8185 (mm) REVERT: A 226 LEU cc_start: 0.8949 (tp) cc_final: 0.8516 (mt) REVERT: A 235 ILE cc_start: 0.7902 (mt) cc_final: 0.7689 (mt) REVERT: A 357 ARG cc_start: 0.8201 (ttp80) cc_final: 0.7810 (ttp80) REVERT: A 366 SER cc_start: 0.8919 (m) cc_final: 0.8569 (p) REVERT: A 386 LYS cc_start: 0.8048 (mmtm) cc_final: 0.7246 (mmtm) REVERT: A 392 PHE cc_start: 0.7762 (m-80) cc_final: 0.7474 (m-10) REVERT: A 402 ILE cc_start: 0.8308 (mp) cc_final: 0.7822 (mp) REVERT: A 403 ARG cc_start: 0.7066 (ptm-80) cc_final: 0.6139 (ptm-80) REVERT: A 406 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7143 (mt-10) REVERT: H 6 GLU cc_start: 0.7822 (mp0) cc_final: 0.7442 (mp0) REVERT: H 13 GLN cc_start: 0.7042 (mm-40) cc_final: 0.6694 (mm-40) REVERT: H 27 PHE cc_start: 0.7967 (p90) cc_final: 0.7374 (p90) REVERT: H 76 LYS cc_start: 0.7504 (mtmm) cc_final: 0.7272 (mtmm) REVERT: H 82 GLN cc_start: 0.7548 (tp40) cc_final: 0.7323 (tp40) REVERT: H 84 ASN cc_start: 0.7164 (m-40) cc_final: 0.6887 (m-40) REVERT: H 89 GLU cc_start: 0.7537 (pp20) cc_final: 0.7240 (tm-30) REVERT: H 98 LYS cc_start: 0.8235 (ptmm) cc_final: 0.7881 (ptmm) REVERT: H 100 ASP cc_start: 0.7668 (t0) cc_final: 0.7328 (t0) REVERT: H 123 THR cc_start: 0.8440 (m) cc_final: 0.7880 (p) REVERT: H 125 VAL cc_start: 0.8793 (p) cc_final: 0.8521 (m) REVERT: H 138 PHE cc_start: 0.8020 (m-80) cc_final: 0.7686 (m-80) REVERT: H 217 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8504 (mtpp) REVERT: H 222 LYS cc_start: 0.7867 (tptp) cc_final: 0.7466 (tppt) REVERT: H 226 LYS cc_start: 0.8375 (tptt) cc_final: 0.8101 (tptp) REVERT: L 13 LEU cc_start: 0.7897 (mm) cc_final: 0.7537 (mm) REVERT: L 39 GLN cc_start: 0.7941 (tp40) cc_final: 0.7429 (tp40) REVERT: L 46 ARG cc_start: 0.8301 (ttp80) cc_final: 0.8083 (ttp-170) REVERT: L 50 TYR cc_start: 0.7363 (p90) cc_final: 0.6640 (p90) REVERT: L 61 ASP cc_start: 0.7196 (t0) cc_final: 0.6843 (t0) REVERT: L 72 PHE cc_start: 0.7405 (m-80) cc_final: 0.7173 (m-80) REVERT: L 126 GLN cc_start: 0.9040 (tt0) cc_final: 0.8709 (tt0) REVERT: L 128 LYS cc_start: 0.8626 (tptm) cc_final: 0.8227 (tptm) REVERT: L 162 GLN cc_start: 0.8003 (tp-100) cc_final: 0.7621 (tp-100) REVERT: L 207 VAL cc_start: 0.7791 (p) cc_final: 0.7522 (t) outliers start: 1 outliers final: 0 residues processed: 332 average time/residue: 0.2437 time to fit residues: 106.7838 Evaluate side-chains 306 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN L 91 GLN ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8740 Z= 0.210 Angle : 0.662 12.468 11897 Z= 0.339 Chirality : 0.048 0.431 1337 Planarity : 0.005 0.079 1518 Dihedral : 7.363 76.832 1352 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.21 % Allowed : 1.82 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.25), residues: 1058 helix: -0.73 (0.66), residues: 61 sheet: 0.14 (0.26), residues: 373 loop : -0.95 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 353 HIS 0.006 0.001 HIS A 207 PHE 0.024 0.002 PHE A 329 TYR 0.023 0.002 TYR H 114 ARG 0.004 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 315 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7386 (p90) cc_final: 0.7038 (p90) REVERT: A 137 ASN cc_start: 0.8383 (t0) cc_final: 0.8114 (t0) REVERT: A 204 TYR cc_start: 0.6963 (m-80) cc_final: 0.6156 (m-80) REVERT: A 206 LYS cc_start: 0.8648 (tppt) cc_final: 0.8198 (tptp) REVERT: A 216 LEU cc_start: 0.8537 (mt) cc_final: 0.7980 (mm) REVERT: A 226 LEU cc_start: 0.8959 (tp) cc_final: 0.8510 (mt) REVERT: A 235 ILE cc_start: 0.7937 (mt) cc_final: 0.7686 (mt) REVERT: A 356 LYS cc_start: 0.8741 (tptp) cc_final: 0.8491 (tptp) REVERT: A 366 SER cc_start: 0.8907 (m) cc_final: 0.8496 (p) REVERT: A 386 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7212 (mmtm) REVERT: A 392 PHE cc_start: 0.7682 (m-80) cc_final: 0.7359 (m-10) REVERT: A 402 ILE cc_start: 0.8205 (mp) cc_final: 0.7912 (mp) REVERT: A 403 ARG cc_start: 0.6951 (ptm-80) cc_final: 0.6469 (ptm-80) REVERT: A 468 ILE cc_start: 0.8730 (pt) cc_final: 0.8343 (mm) REVERT: A 533 LEU cc_start: 0.7500 (tt) cc_final: 0.7254 (pp) REVERT: A 558 LYS cc_start: 0.7034 (ttmm) cc_final: 0.6799 (tptt) REVERT: H 6 GLU cc_start: 0.7813 (mp0) cc_final: 0.7421 (mp0) REVERT: H 27 PHE cc_start: 0.7961 (p90) cc_final: 0.7415 (p90) REVERT: H 34 MET cc_start: 0.8114 (mmm) cc_final: 0.7844 (mmm) REVERT: H 59 TYR cc_start: 0.6646 (t80) cc_final: 0.6420 (t80) REVERT: H 82 GLN cc_start: 0.7474 (tp40) cc_final: 0.7163 (tp40) REVERT: H 84 ASN cc_start: 0.7239 (m-40) cc_final: 0.6852 (m-40) REVERT: H 89 GLU cc_start: 0.7564 (pp20) cc_final: 0.7349 (tm-30) REVERT: H 98 LYS cc_start: 0.8144 (ptmm) cc_final: 0.7535 (ptmm) REVERT: H 100 ASP cc_start: 0.7612 (t0) cc_final: 0.7192 (t0) REVERT: H 117 ASP cc_start: 0.7666 (p0) cc_final: 0.7411 (p0) REVERT: H 123 THR cc_start: 0.8417 (m) cc_final: 0.7844 (p) REVERT: H 138 PHE cc_start: 0.7972 (m-80) cc_final: 0.7517 (m-80) REVERT: H 159 LYS cc_start: 0.8112 (tptt) cc_final: 0.7508 (tptt) REVERT: H 166 VAL cc_start: 0.8744 (p) cc_final: 0.8399 (m) REVERT: H 187 GLN cc_start: 0.7524 (pt0) cc_final: 0.6019 (pt0) REVERT: H 210 TYR cc_start: 0.5527 (m-80) cc_final: 0.5228 (m-80) REVERT: H 217 LYS cc_start: 0.8678 (mtpp) cc_final: 0.8466 (mtpp) REVERT: H 222 LYS cc_start: 0.7853 (tptp) cc_final: 0.7453 (tppt) REVERT: H 226 LYS cc_start: 0.8383 (tptt) cc_final: 0.8059 (tptp) REVERT: L 39 GLN cc_start: 0.7827 (tp40) cc_final: 0.7320 (tp40) REVERT: L 40 LYS cc_start: 0.8673 (ptpp) cc_final: 0.8395 (ptpp) REVERT: L 50 TYR cc_start: 0.7293 (p90) cc_final: 0.6695 (p90) REVERT: L 61 ASP cc_start: 0.7163 (t0) cc_final: 0.6847 (t0) REVERT: L 72 PHE cc_start: 0.7391 (m-80) cc_final: 0.7186 (m-80) REVERT: L 126 GLN cc_start: 0.9044 (tt0) cc_final: 0.8664 (tt0) REVERT: L 128 LYS cc_start: 0.8624 (tptm) cc_final: 0.8183 (tptm) REVERT: L 162 GLN cc_start: 0.7973 (tp-100) cc_final: 0.7638 (tp-100) REVERT: L 207 VAL cc_start: 0.7832 (p) cc_final: 0.7619 (t) outliers start: 2 outliers final: 0 residues processed: 315 average time/residue: 0.2204 time to fit residues: 92.8024 Evaluate side-chains 290 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8740 Z= 0.303 Angle : 0.734 12.166 11897 Z= 0.381 Chirality : 0.049 0.455 1337 Planarity : 0.005 0.084 1518 Dihedral : 7.744 78.157 1352 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.21 % Allowed : 1.18 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % 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: -1.09 (0.25), residues: 1058 helix: -0.97 (0.64), residues: 60 sheet: -0.04 (0.26), residues: 367 loop : -1.13 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 353 HIS 0.005 0.001 HIS L 200 PHE 0.024 0.002 PHE A 275 TYR 0.023 0.002 TYR L 33 ARG 0.010 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 303 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7399 (p90) cc_final: 0.7022 (p90) REVERT: A 38 TYR cc_start: 0.8249 (m-80) cc_final: 0.7925 (m-80) REVERT: A 137 ASN cc_start: 0.8475 (t0) cc_final: 0.8203 (t0) REVERT: A 204 TYR cc_start: 0.6947 (m-80) cc_final: 0.6394 (m-80) REVERT: A 216 LEU cc_start: 0.8630 (mt) cc_final: 0.8093 (mm) REVERT: A 226 LEU cc_start: 0.8971 (tp) cc_final: 0.8510 (mt) REVERT: A 246 ARG cc_start: 0.7538 (mtp85) cc_final: 0.6977 (mtp85) REVERT: A 310 LYS cc_start: 0.8287 (ptpp) cc_final: 0.8061 (ptpp) REVERT: A 366 SER cc_start: 0.8951 (m) cc_final: 0.8582 (p) REVERT: A 386 LYS cc_start: 0.8232 (mmtm) cc_final: 0.7398 (mmtm) REVERT: A 392 PHE cc_start: 0.7603 (m-80) cc_final: 0.7401 (m-10) REVERT: A 402 ILE cc_start: 0.8255 (mp) cc_final: 0.7724 (mp) REVERT: A 403 ARG cc_start: 0.6928 (ptm-80) cc_final: 0.6391 (ptm-80) REVERT: A 453 TYR cc_start: 0.7040 (p90) cc_final: 0.6543 (p90) REVERT: A 611 LEU cc_start: 0.7435 (tp) cc_final: 0.7197 (pp) REVERT: H 6 GLU cc_start: 0.7826 (mp0) cc_final: 0.7403 (mp0) REVERT: H 13 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6822 (mm-40) REVERT: H 27 PHE cc_start: 0.7995 (p90) cc_final: 0.7355 (p90) REVERT: H 28 ILE cc_start: 0.8677 (mp) cc_final: 0.8468 (mp) REVERT: H 34 MET cc_start: 0.7915 (mmm) cc_final: 0.7697 (mmm) REVERT: H 39 GLN cc_start: 0.7643 (tt0) cc_final: 0.7434 (tt0) REVERT: H 59 TYR cc_start: 0.6902 (t80) cc_final: 0.6550 (t80) REVERT: H 97 THR cc_start: 0.7297 (p) cc_final: 0.6902 (t) REVERT: H 98 LYS cc_start: 0.8330 (ptmm) cc_final: 0.7683 (ptmm) REVERT: H 100 ASP cc_start: 0.7599 (t0) cc_final: 0.7320 (t0) REVERT: H 117 ASP cc_start: 0.7792 (p0) cc_final: 0.7507 (p0) REVERT: H 123 THR cc_start: 0.8425 (m) cc_final: 0.7812 (p) REVERT: H 138 PHE cc_start: 0.7893 (m-80) cc_final: 0.7530 (m-80) REVERT: H 159 LYS cc_start: 0.8146 (tptt) cc_final: 0.7572 (tptt) REVERT: H 186 LEU cc_start: 0.7915 (pp) cc_final: 0.7698 (pp) REVERT: H 187 GLN cc_start: 0.7675 (pt0) cc_final: 0.6142 (pt0) REVERT: H 210 TYR cc_start: 0.5567 (m-80) cc_final: 0.5180 (m-10) REVERT: H 217 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8488 (mtpp) REVERT: H 226 LYS cc_start: 0.8457 (tptt) cc_final: 0.8168 (tptp) REVERT: L 39 GLN cc_start: 0.7883 (tp40) cc_final: 0.7334 (tp40) REVERT: L 40 LYS cc_start: 0.8666 (ptpp) cc_final: 0.8420 (ptpp) REVERT: L 50 TYR cc_start: 0.7298 (p90) cc_final: 0.6617 (p90) REVERT: L 61 ASP cc_start: 0.7289 (t0) cc_final: 0.6998 (t70) REVERT: L 109 LYS cc_start: 0.7474 (ptpp) cc_final: 0.7256 (pttt) REVERT: L 128 LYS cc_start: 0.8669 (tptm) cc_final: 0.8314 (tptm) REVERT: L 180 THR cc_start: 0.8103 (p) cc_final: 0.7099 (p) outliers start: 2 outliers final: 0 residues processed: 304 average time/residue: 0.2427 time to fit residues: 97.8830 Evaluate side-chains 295 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 0.0170 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 chunk 93 optimal weight: 0.2980 chunk 98 optimal weight: 0.7980 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN L 91 GLN ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8740 Z= 0.200 Angle : 0.682 10.452 11897 Z= 0.349 Chirality : 0.049 0.439 1337 Planarity : 0.005 0.073 1518 Dihedral : 7.486 79.874 1352 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.21 % Allowed : 0.75 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1058 helix: -0.57 (0.69), residues: 60 sheet: 0.10 (0.26), residues: 374 loop : -1.00 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 353 HIS 0.007 0.001 HIS L 200 PHE 0.026 0.002 PHE A 329 TYR 0.016 0.001 TYR L 33 ARG 0.006 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 311 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7295 (p90) cc_final: 0.6797 (p90) REVERT: A 38 TYR cc_start: 0.8218 (m-80) cc_final: 0.7684 (m-10) REVERT: A 64 TRP cc_start: 0.6366 (t60) cc_final: 0.6149 (t60) REVERT: A 137 ASN cc_start: 0.8444 (t0) cc_final: 0.8164 (t0) REVERT: A 196 ASN cc_start: 0.8347 (t0) cc_final: 0.8093 (t0) REVERT: A 204 TYR cc_start: 0.6703 (m-80) cc_final: 0.5956 (m-80) REVERT: A 216 LEU cc_start: 0.8634 (mt) cc_final: 0.7974 (mm) REVERT: A 226 LEU cc_start: 0.8978 (tp) cc_final: 0.8603 (mt) REVERT: A 310 LYS cc_start: 0.8180 (ptpp) cc_final: 0.7745 (ptpp) REVERT: A 321 GLN cc_start: 0.7554 (tt0) cc_final: 0.7110 (tt0) REVERT: A 357 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7944 (ttp80) REVERT: A 366 SER cc_start: 0.8888 (m) cc_final: 0.8477 (p) REVERT: A 386 LYS cc_start: 0.8142 (mmtm) cc_final: 0.7316 (mmtm) REVERT: A 392 PHE cc_start: 0.7618 (m-80) cc_final: 0.7406 (m-10) REVERT: A 402 ILE cc_start: 0.8215 (mp) cc_final: 0.7916 (mp) REVERT: A 403 ARG cc_start: 0.6866 (ptm-80) cc_final: 0.6520 (ptm-80) REVERT: A 418 ILE cc_start: 0.8300 (mp) cc_final: 0.8049 (mm) REVERT: A 453 TYR cc_start: 0.6882 (p90) cc_final: 0.6199 (p90) REVERT: H 6 GLU cc_start: 0.7821 (mp0) cc_final: 0.7405 (mp0) REVERT: H 13 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6828 (mm-40) REVERT: H 27 PHE cc_start: 0.7951 (p90) cc_final: 0.7378 (p90) REVERT: H 39 GLN cc_start: 0.7559 (tt0) cc_final: 0.7351 (tt0) REVERT: H 67 ARG cc_start: 0.6412 (mtp180) cc_final: 0.5944 (mtp180) REVERT: H 90 ASP cc_start: 0.8508 (m-30) cc_final: 0.8242 (m-30) REVERT: H 97 THR cc_start: 0.7403 (p) cc_final: 0.6958 (t) REVERT: H 98 LYS cc_start: 0.8212 (ptmm) cc_final: 0.7551 (ptmm) REVERT: H 100 ASP cc_start: 0.7557 (t0) cc_final: 0.7229 (t0) REVERT: H 117 ASP cc_start: 0.7704 (p0) cc_final: 0.7385 (p0) REVERT: H 159 LYS cc_start: 0.8095 (tptt) cc_final: 0.7544 (tptt) REVERT: H 166 VAL cc_start: 0.8821 (p) cc_final: 0.8452 (m) REVERT: H 187 GLN cc_start: 0.7480 (pt0) cc_final: 0.6042 (pt0) REVERT: H 210 TYR cc_start: 0.5529 (m-80) cc_final: 0.5106 (m-80) REVERT: H 222 LYS cc_start: 0.7894 (tptp) cc_final: 0.7475 (tppt) REVERT: H 226 LYS cc_start: 0.8443 (tptt) cc_final: 0.8152 (tptp) REVERT: L 39 GLN cc_start: 0.7840 (tp40) cc_final: 0.7334 (tp40) REVERT: L 50 TYR cc_start: 0.7262 (p90) cc_final: 0.6645 (p90) REVERT: L 72 PHE cc_start: 0.7552 (m-80) cc_final: 0.6888 (m-80) REVERT: L 126 GLN cc_start: 0.9064 (tt0) cc_final: 0.8580 (tt0) REVERT: L 128 LYS cc_start: 0.8690 (tptm) cc_final: 0.8319 (tptm) REVERT: L 162 GLN cc_start: 0.6756 (mp10) cc_final: 0.6387 (mp10) REVERT: L 180 THR cc_start: 0.7943 (p) cc_final: 0.6934 (p) REVERT: L 207 VAL cc_start: 0.8128 (t) cc_final: 0.7756 (t) outliers start: 2 outliers final: 0 residues processed: 311 average time/residue: 0.2403 time to fit residues: 97.5705 Evaluate side-chains 290 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.5844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 8740 Z= 0.299 Angle : 0.743 13.582 11897 Z= 0.384 Chirality : 0.049 0.459 1337 Planarity : 0.005 0.083 1518 Dihedral : 7.615 81.371 1352 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.11 % Allowed : 0.96 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % 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: -1.09 (0.25), residues: 1058 helix: -0.78 (0.66), residues: 60 sheet: -0.07 (0.26), residues: 370 loop : -1.13 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 353 HIS 0.006 0.001 HIS L 200 PHE 0.021 0.002 PHE A 429 TYR 0.025 0.002 TYR H 114 ARG 0.011 0.001 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 302 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7209 (p90) cc_final: 0.6789 (p90) REVERT: A 38 TYR cc_start: 0.8327 (m-80) cc_final: 0.8024 (m-80) REVERT: A 40 ASP cc_start: 0.8282 (p0) cc_final: 0.8071 (p0) REVERT: A 137 ASN cc_start: 0.8487 (t0) cc_final: 0.8176 (t0) REVERT: A 196 ASN cc_start: 0.8396 (t0) cc_final: 0.8161 (t0) REVERT: A 204 TYR cc_start: 0.6695 (m-80) cc_final: 0.6159 (m-80) REVERT: A 206 LYS cc_start: 0.8316 (tptp) cc_final: 0.8009 (tmtt) REVERT: A 216 LEU cc_start: 0.8707 (mt) cc_final: 0.8152 (mm) REVERT: A 226 LEU cc_start: 0.8959 (tp) cc_final: 0.8552 (mt) REVERT: A 310 LYS cc_start: 0.8330 (ptpp) cc_final: 0.7898 (ptpp) REVERT: A 366 SER cc_start: 0.8909 (m) cc_final: 0.8582 (p) REVERT: A 386 LYS cc_start: 0.8238 (mmtm) cc_final: 0.7414 (mmtm) REVERT: A 402 ILE cc_start: 0.8202 (mp) cc_final: 0.7837 (mp) REVERT: A 403 ARG cc_start: 0.6871 (ptm-80) cc_final: 0.6577 (ptm-80) REVERT: H 6 GLU cc_start: 0.7827 (mp0) cc_final: 0.7462 (mp0) REVERT: H 13 GLN cc_start: 0.7263 (mm-40) cc_final: 0.6932 (mm-40) REVERT: H 27 PHE cc_start: 0.7988 (p90) cc_final: 0.7382 (p90) REVERT: H 28 ILE cc_start: 0.8686 (mp) cc_final: 0.8475 (mp) REVERT: H 34 MET cc_start: 0.7926 (mmm) cc_final: 0.7688 (mmm) REVERT: H 39 GLN cc_start: 0.7699 (tt0) cc_final: 0.7441 (tt0) REVERT: H 90 ASP cc_start: 0.8379 (m-30) cc_final: 0.8010 (m-30) REVERT: H 97 THR cc_start: 0.7373 (p) cc_final: 0.6879 (t) REVERT: H 98 LYS cc_start: 0.8382 (ptmm) cc_final: 0.7765 (ptmm) REVERT: H 100 ASP cc_start: 0.7692 (t0) cc_final: 0.7360 (t0) REVERT: H 123 THR cc_start: 0.8418 (m) cc_final: 0.7766 (p) REVERT: H 159 LYS cc_start: 0.8260 (tptt) cc_final: 0.7677 (tptt) REVERT: H 187 GLN cc_start: 0.7647 (pt0) cc_final: 0.7012 (pt0) REVERT: H 210 TYR cc_start: 0.5813 (m-80) cc_final: 0.5444 (m-10) REVERT: H 217 LYS cc_start: 0.8860 (tttp) cc_final: 0.8610 (tttp) REVERT: L 39 GLN cc_start: 0.7891 (tp40) cc_final: 0.7370 (tp40) REVERT: L 40 LYS cc_start: 0.8695 (ptpp) cc_final: 0.8413 (ptpp) REVERT: L 50 TYR cc_start: 0.7344 (p90) cc_final: 0.6606 (p90) REVERT: L 72 PHE cc_start: 0.7580 (m-80) cc_final: 0.7183 (m-80) REVERT: L 76 ILE cc_start: 0.7903 (tp) cc_final: 0.7692 (tp) REVERT: L 126 GLN cc_start: 0.9055 (tt0) cc_final: 0.8653 (tt0) REVERT: L 128 LYS cc_start: 0.8829 (tptm) cc_final: 0.8335 (tptm) REVERT: L 162 GLN cc_start: 0.6840 (mp10) cc_final: 0.6439 (mp10) REVERT: L 180 THR cc_start: 0.7997 (p) cc_final: 0.6818 (p) REVERT: L 207 VAL cc_start: 0.8290 (t) cc_final: 0.7900 (t) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.2401 time to fit residues: 95.7526 Evaluate side-chains 286 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 67 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8740 Z= 0.246 Angle : 0.705 10.407 11897 Z= 0.363 Chirality : 0.049 0.453 1337 Planarity : 0.005 0.076 1518 Dihedral : 7.555 83.486 1352 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.21 % Allowed : 0.32 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % 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: -1.03 (0.25), residues: 1058 helix: -0.62 (0.68), residues: 60 sheet: -0.18 (0.26), residues: 390 loop : -1.01 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 64 HIS 0.007 0.002 HIS L 200 PHE 0.018 0.002 PHE A 106 TYR 0.024 0.002 TYR H 114 ARG 0.009 0.001 ARG A 577 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 301 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.8147 (m) cc_final: 0.7796 (t) REVERT: A 37 TYR cc_start: 0.7321 (p90) cc_final: 0.6779 (p90) REVERT: A 38 TYR cc_start: 0.8306 (m-80) cc_final: 0.7803 (m-80) REVERT: A 137 ASN cc_start: 0.8431 (t0) cc_final: 0.8165 (t0) REVERT: A 175 PHE cc_start: 0.7181 (p90) cc_final: 0.6961 (p90) REVERT: A 196 ASN cc_start: 0.8383 (t0) cc_final: 0.8172 (t0) REVERT: A 216 LEU cc_start: 0.8754 (mt) cc_final: 0.7921 (mm) REVERT: A 226 LEU cc_start: 0.8960 (tp) cc_final: 0.8551 (mt) REVERT: A 310 LYS cc_start: 0.8300 (ptpp) cc_final: 0.7839 (ptpp) REVERT: A 321 GLN cc_start: 0.7297 (tt0) cc_final: 0.7091 (tt0) REVERT: A 338 PHE cc_start: 0.7646 (m-80) cc_final: 0.7425 (m-80) REVERT: A 366 SER cc_start: 0.8882 (m) cc_final: 0.8527 (p) REVERT: A 386 LYS cc_start: 0.8126 (mmtm) cc_final: 0.7430 (mmtm) REVERT: A 402 ILE cc_start: 0.8177 (mp) cc_final: 0.7713 (mp) REVERT: A 403 ARG cc_start: 0.6713 (ptm-80) cc_final: 0.5854 (ptm-80) REVERT: A 528 LYS cc_start: 0.8309 (tptp) cc_final: 0.7771 (tppp) REVERT: A 529 LYS cc_start: 0.8126 (mmpt) cc_final: 0.7910 (mmpt) REVERT: H 6 GLU cc_start: 0.7844 (mp0) cc_final: 0.7443 (mp0) REVERT: H 13 GLN cc_start: 0.7212 (mm-40) cc_final: 0.6800 (mm-40) REVERT: H 27 PHE cc_start: 0.7982 (p90) cc_final: 0.7370 (p90) REVERT: H 34 MET cc_start: 0.7967 (mmm) cc_final: 0.7696 (mmm) REVERT: H 39 GLN cc_start: 0.7618 (tt0) cc_final: 0.7333 (tt0) REVERT: H 97 THR cc_start: 0.7432 (p) cc_final: 0.6926 (t) REVERT: H 98 LYS cc_start: 0.8246 (ptmm) cc_final: 0.7640 (ptmm) REVERT: H 100 ASP cc_start: 0.7642 (t0) cc_final: 0.7403 (t0) REVERT: H 123 THR cc_start: 0.8438 (m) cc_final: 0.7789 (p) REVERT: H 138 PHE cc_start: 0.8114 (m-80) cc_final: 0.7506 (m-80) REVERT: H 159 LYS cc_start: 0.8155 (tptt) cc_final: 0.7621 (tptt) REVERT: H 170 TRP cc_start: 0.7069 (m100) cc_final: 0.6813 (m100) REVERT: H 187 GLN cc_start: 0.7582 (pt0) cc_final: 0.6982 (pt0) REVERT: H 210 TYR cc_start: 0.5898 (m-80) cc_final: 0.5397 (m-10) REVERT: H 217 LYS cc_start: 0.8881 (tttp) cc_final: 0.8635 (tttp) REVERT: H 226 LYS cc_start: 0.8284 (tptt) cc_final: 0.8077 (tptp) REVERT: L 39 GLN cc_start: 0.7899 (tp40) cc_final: 0.7377 (tp40) REVERT: L 50 TYR cc_start: 0.7288 (p90) cc_final: 0.6577 (p90) REVERT: L 72 PHE cc_start: 0.7589 (m-80) cc_final: 0.7170 (m-80) REVERT: L 76 ILE cc_start: 0.7856 (tp) cc_final: 0.7606 (tp) REVERT: L 126 GLN cc_start: 0.9127 (tt0) cc_final: 0.8709 (tt0) REVERT: L 128 LYS cc_start: 0.8812 (tptm) cc_final: 0.8337 (tptm) REVERT: L 145 GLU cc_start: 0.8766 (mp0) cc_final: 0.8470 (mp0) REVERT: L 162 GLN cc_start: 0.6908 (mp10) cc_final: 0.6475 (mp10) REVERT: L 180 THR cc_start: 0.7951 (p) cc_final: 0.6749 (p) REVERT: L 207 VAL cc_start: 0.8296 (t) cc_final: 0.7921 (t) outliers start: 2 outliers final: 0 residues processed: 301 average time/residue: 0.2313 time to fit residues: 92.8938 Evaluate side-chains 281 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 85 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.129888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.102046 restraints weight = 19133.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.106379 restraints weight = 10855.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.109371 restraints weight = 7163.421| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8740 Z= 0.284 Angle : 0.759 16.117 11897 Z= 0.392 Chirality : 0.051 0.461 1337 Planarity : 0.006 0.088 1518 Dihedral : 7.712 85.130 1352 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.21 % Allowed : 0.11 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.17 (0.25), residues: 1058 helix: -1.02 (0.66), residues: 60 sheet: -0.25 (0.25), residues: 385 loop : -1.08 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP A 64 HIS 0.018 0.002 HIS A 66 PHE 0.032 0.002 PHE A 55 TYR 0.021 0.002 TYR L 33 ARG 0.010 0.001 ARG A 577 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2683.09 seconds wall clock time: 49 minutes 19.72 seconds (2959.72 seconds total)