Starting phenix.real_space_refine on Fri Dec 8 14:04:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/12_2023/7zbu_14591_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/12_2023/7zbu_14591.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/12_2023/7zbu_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_14591/12_2023/7zbu_14591_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/12_2023/7zbu_14591_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/12_2023/7zbu_14591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/12_2023/7zbu_14591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/12_2023/7zbu_14591_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zbu_14591/12_2023/7zbu_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.81, per 1000 atoms: 0.56 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: 3.16 Conformation dependent library (CDL) restraints added in 1.7 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: 2.01 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: 2.84 Time building geometry restraints manager: 3.44 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: 2.280 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: 8.110 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 26.990 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- 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 : 0.953 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 outliers start: 2 outliers final: 0 residues processed: 373 average time/residue: 0.2357 time to fit residues: 115.5340 Evaluate side-chains 319 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3590 ------------------------------------------------------------------------------- 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: 3.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 0.1980 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 0.0570 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 82 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8740 Z= 0.220 Angle : 0.676 7.917 11897 Z= 0.344 Chirality : 0.049 0.472 1337 Planarity : 0.005 0.045 1518 Dihedral : 7.432 78.628 1352 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.43 % Allowed : 2.89 % Favored : 96.68 % 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: -0.41 (0.78), residues: 47 sheet: 0.52 (0.26), residues: 359 loop : -0.75 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 436 HIS 0.013 0.002 HIS A 207 PHE 0.030 0.002 PHE A 562 TYR 0.022 0.002 TYR A 365 ARG 0.005 0.001 ARG A 328 *********************** 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 351 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 347 time to evaluate : 0.986 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 outliers start: 4 outliers final: 0 residues processed: 349 average time/residue: 0.2360 time to fit residues: 108.4914 Evaluate side-chains 307 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3837 ------------------------------------------------------------------------------- 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: 0.8980 chunk 80 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 97 optimal weight: 0.0970 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 96 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- 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 540 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN L 90 GLN L 91 GLN ** L 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8740 Z= 0.230 Angle : 0.680 7.823 11897 Z= 0.347 Chirality : 0.048 0.440 1337 Planarity : 0.005 0.042 1518 Dihedral : 7.319 84.111 1352 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.43 % Allowed : 3.21 % Favored : 96.36 % 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: -0.46 (0.25), residues: 1058 helix: -0.76 (0.75), residues: 46 sheet: 0.44 (0.26), residues: 355 loop : -0.70 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 119 HIS 0.009 0.001 HIS A 207 PHE 0.023 0.002 PHE A 55 TYR 0.021 0.002 TYR L 175 ARG 0.005 0.001 ARG H 87 *********************** 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 351 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 347 time to evaluate : 0.879 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 outliers start: 4 outliers final: 0 residues processed: 348 average time/residue: 0.2308 time to fit residues: 106.0640 Evaluate side-chains 308 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3173 ------------------------------------------------------------------------------- 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: 0.3980 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 27 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 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: 0.6818 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8740 Z= 0.253 Angle : 0.729 17.534 11897 Z= 0.372 Chirality : 0.049 0.427 1337 Planarity : 0.005 0.044 1518 Dihedral : 7.346 88.683 1352 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.43 % Allowed : 3.21 % Favored : 96.36 % 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: -0.60 (0.25), residues: 1058 helix: -0.83 (0.67), residues: 62 sheet: 0.44 (0.26), residues: 355 loop : -0.85 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 64 HIS 0.008 0.001 HIS A 207 PHE 0.038 0.002 PHE A 275 TYR 0.019 0.002 TYR H 101 ARG 0.005 0.001 ARG L 46 *********************** 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 349 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 345 time to evaluate : 0.974 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 outliers start: 4 outliers final: 2 residues processed: 346 average time/residue: 0.2385 time to fit residues: 110.2621 Evaluate side-chains 307 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 305 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0983 time to fit residues: 1.6872 ------------------------------------------------------------------------------- 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: 0.7980 chunk 58 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 42 optimal weight: 0.0020 chunk 88 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8740 Z= 0.247 Angle : 0.746 21.535 11897 Z= 0.381 Chirality : 0.050 0.425 1337 Planarity : 0.005 0.044 1518 Dihedral : 7.276 86.895 1352 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.21 % Allowed : 2.57 % Favored : 97.22 % 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: -0.72 (0.25), residues: 1058 helix: -0.99 (0.64), residues: 60 sheet: 0.35 (0.26), residues: 344 loop : -0.90 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 64 HIS 0.005 0.001 HIS A 207 PHE 0.040 0.002 PHE A 400 TYR 0.017 0.002 TYR L 188 ARG 0.012 0.001 ARG A 34 *********************** 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 324 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 322 time to evaluate : 0.982 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 outliers start: 2 outliers final: 1 residues processed: 324 average time/residue: 0.2397 time to fit residues: 102.0570 Evaluate side-chains 300 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0751 time to fit residues: 1.3698 ------------------------------------------------------------------------------- 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: 1.9990 chunk 93 optimal weight: 0.0070 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 0.0270 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 54 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 overall best weight: 0.3854 ------------------------------------------------------------------------------- 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 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS H 187 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8740 Z= 0.197 Angle : 0.723 21.215 11897 Z= 0.367 Chirality : 0.049 0.405 1337 Planarity : 0.004 0.045 1518 Dihedral : 7.061 84.353 1352 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.32 % Allowed : 1.50 % Favored : 98.18 % 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: -0.69 (0.25), residues: 1058 helix: -1.01 (0.63), residues: 61 sheet: 0.32 (0.26), residues: 355 loop : -0.86 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 353 HIS 0.005 0.001 HIS A 655 PHE 0.023 0.002 PHE A 400 TYR 0.017 0.001 TYR A 505 ARG 0.006 0.001 ARG A 403 *********************** 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 323 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 320 time to evaluate : 0.878 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: symmetry clash outliers start: 3 outliers final: 1 residues processed: 322 average time/residue: 0.2384 time to fit residues: 101.2257 Evaluate side-chains 289 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 288 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0830 time to fit residues: 1.5096 ------------------------------------------------------------------------------- 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: 4.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 0.2980 chunk 47 optimal weight: 6.9990 chunk 63 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 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 66 HIS ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 556 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 GLN L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8740 Z= 0.223 Angle : 0.731 22.237 11897 Z= 0.371 Chirality : 0.049 0.410 1337 Planarity : 0.005 0.043 1518 Dihedral : 7.071 82.073 1352 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.21 % Allowed : 1.50 % Favored : 98.29 % 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: -0.74 (0.25), residues: 1058 helix: -0.90 (0.66), residues: 62 sheet: 0.15 (0.26), residues: 361 loop : -0.82 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 64 HIS 0.010 0.001 HIS A 66 PHE 0.027 0.002 PHE A 55 TYR 0.020 0.002 TYR H 114 ARG 0.005 0.001 ARG A 34 *********************** 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 316 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 314 time to evaluate : 0.894 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 315 average time/residue: 0.2505 time to fit residues: 103.6335 Evaluate side-chains 292 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1949 ------------------------------------------------------------------------------- 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: 0.6980 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 218 GLN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 8740 Z= 0.336 Angle : 0.822 23.033 11897 Z= 0.423 Chirality : 0.052 0.487 1337 Planarity : 0.005 0.054 1518 Dihedral : 7.417 77.751 1352 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % 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: -1.13 (0.25), residues: 1058 helix: -1.04 (0.63), residues: 62 sheet: -0.12 (0.25), residues: 380 loop : -1.12 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 64 HIS 0.017 0.002 HIS A 66 PHE 0.067 0.003 PHE A 275 TYR 0.027 0.002 TYR H 114 ARG 0.006 0.001 ARG A 328 *********************** 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 314 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 1.027 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.2386 time to fit residues: 98.9417 Evaluate side-chains 293 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3618 ------------------------------------------------------------------------------- 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: 0.9990 chunk 96 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 563 GLN ** 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 6 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8740 Z= 0.254 Angle : 0.779 19.022 11897 Z= 0.399 Chirality : 0.051 0.461 1337 Planarity : 0.005 0.049 1518 Dihedral : 7.335 76.466 1352 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % Favored : 99.57 % 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: -1.16 (0.25), residues: 1058 helix: -0.85 (0.65), residues: 62 sheet: -0.24 (0.25), residues: 383 loop : -1.10 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 64 HIS 0.012 0.001 HIS A 66 PHE 0.028 0.002 PHE H 138 TYR 0.023 0.002 TYR H 114 ARG 0.008 0.001 ARG H 67 *********************** 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 302 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 301 time to evaluate : 1.005 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 outliers start: 1 outliers final: 0 residues processed: 301 average time/residue: 0.2441 time to fit residues: 96.7333 Evaluate side-chains 278 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2931 ------------------------------------------------------------------------------- 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: 3.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 556 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN L 38 GLN ** L 90 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.6015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8740 Z= 0.284 Angle : 0.808 24.308 11897 Z= 0.412 Chirality : 0.051 0.475 1337 Planarity : 0.005 0.101 1518 Dihedral : 7.375 75.747 1352 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.21 % Allowed : 0.53 % Favored : 99.25 % 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: -1.21 (0.25), residues: 1058 helix: -0.85 (0.66), residues: 61 sheet: -0.19 (0.26), residues: 373 loop : -1.19 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 64 HIS 0.003 0.001 HIS A 207 PHE 0.023 0.002 PHE A 106 TYR 0.023 0.002 TYR L 33 ARG 0.011 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 294 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 292 time to evaluate : 1.025 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 outliers start: 2 outliers final: 0 residues processed: 292 average time/residue: 0.2503 time to fit residues: 95.5237 Evaluate side-chains 267 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2879 ------------------------------------------------------------------------------- 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: 0.7980 chunk 78 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.129423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.101591 restraints weight = 19264.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105998 restraints weight = 10946.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.109035 restraints weight = 7208.293| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8740 Z= 0.274 Angle : 0.794 18.390 11897 Z= 0.407 Chirality : 0.052 0.466 1337 Planarity : 0.005 0.067 1518 Dihedral : 7.411 75.410 1352 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.11 % Allowed : 0.32 % Favored : 99.57 % 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: -1.30 (0.24), residues: 1058 helix: -1.17 (0.60), residues: 67 sheet: -0.18 (0.26), residues: 375 loop : -1.27 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP H 170 HIS 0.004 0.001 HIS A 207 PHE 0.039 0.002 PHE H 138 TYR 0.021 0.002 TYR L 33 ARG 0.014 0.001 ARG L 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2669.03 seconds wall clock time: 49 minutes 4.76 seconds (2944.76 seconds total)