Starting phenix.real_space_refine on Fri Sep 11 18:42:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6c5v_7344/09_2026/6c5v_7344.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c5v_7344/09_2026/6c5v_7344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6c5v_7344/09_2026/6c5v_7344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c5v_7344/09_2026/6c5v_7344.map" model { file = "/net/cci-nas-00/data/ceres_data/6c5v_7344/09_2026/6c5v_7344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c5v_7344/09_2026/6c5v_7344.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6c5v_7344/09_2026/6c5v_7344.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6c5v_7344/09_2026/6c5v_7344.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.007 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 58 5.16 5 C 6787 2.51 5 N 1749 2.21 5 O 2055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10649 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 5101 Classifications: {'peptide': 655} Link IDs: {'PTRANS': 26, 'TRANS': 628} Chain: "B" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 2 Chain: "C" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1435 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "H" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1615 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1598 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 194} Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.84, per 1000 atoms: 0.27 Number of scatterers: 10649 At special positions: 0 Unit cell: (137.36, 116.96, 127.84, 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 58 16.00 O 2055 8.00 N 1749 7.00 C 6787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 335 " distance=2.04 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 615 " distance=2.04 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 56 " distance=2.05 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 138 " distance=2.02 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 115 " distance=2.08 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 216 " distance=2.01 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 208 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.11 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A 707 " - " ASN A 435 " " NAG A 708 " - " ASN A 549 " " NAG A 709 " - " ASN A 664 " " NAG B 201 " - " ASN B 44 " " NAG B 202 " - " ASN B 53 " " NAG C 301 " - " ASN C 64 " " NAG C 302 " - " ASN C 98 " " NAG C 303 " - " ASN C 173 " " NAG D 1 " - " ASN A 60 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 396.2 milliseconds 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 19 sheets defined 31.7% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 51 through 60 removed outlier: 3.529A pdb=" N LEU A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.149A pdb=" N VAL A 107 " --> pdb=" O ALA A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 131 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 245 through 256 Processing helix chain 'A' and resid 257 through 275 Processing helix chain 'A' and resid 284 through 307 Processing helix chain 'A' and resid 315 through 336 removed outlier: 3.717A pdb=" N ILE A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 357 Processing helix chain 'A' and resid 358 through 359 No H-bonds generated for 'chain 'A' and resid 358 through 359' Processing helix chain 'A' and resid 360 through 367 removed outlier: 4.748A pdb=" N GLY A 365 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 383 Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 391 through 405 Processing helix chain 'A' and resid 414 through 432 removed outlier: 3.700A pdb=" N HIS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 453 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 470 through 475 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 502 through 517 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 529 through 535 Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 636 through 646 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 82 through 96 Processing helix chain 'B' and resid 97 through 100 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'C' and resid 124 through 134 removed outlier: 4.241A pdb=" N PHE C 129 " --> pdb=" O TRP C 125 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN C 130 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 133 " --> pdb=" O PHE C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 154 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 191 through 197 Processing helix chain 'H' and resid 207 through 210 Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'L' and resid 92 through 96 Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 185 through 192 removed outlier: 3.668A pdb=" N HIS L 192 " --> pdb=" O GLN L 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.133A pdb=" N MET A 100 " --> pdb=" O CYS A 120 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU A 122 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL A 102 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 138 removed outlier: 6.749A pdb=" N LEU A 151 " --> pdb=" O MET A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 220 removed outlier: 6.635A pdb=" N LEU A 226 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLN A 220 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 172 " --> pdb=" O MET A 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 541 through 547 Processing sheet with id=AA6, first strand: chain 'A' and resid 601 through 602 removed outlier: 4.984A pdb=" N TYR A 658 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU A 619 " --> pdb=" O THR A 631 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR A 631 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER A 621 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 109 through 111 removed outlier: 3.589A pdb=" N CYS C 214 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS C 121 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS C 212 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 162 through 163 Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.643A pdb=" N ASP H 10 " --> pdb=" O LEU H 114 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AB3, first strand: chain 'H' and resid 126 through 130 removed outlier: 5.862A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER H 183 " --> pdb=" O ALA H 174 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA H 174 " --> pdb=" O SER H 183 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER H 185 " --> pdb=" O PHE H 172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 157 through 160 Processing sheet with id=AB5, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.199A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB7, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.523A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.523A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 157 through 159 removed outlier: 4.365A pdb=" N TRP L 152 " --> pdb=" O VAL L 159 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2582 1.33 - 1.46: 3189 1.46 - 1.59: 5054 1.59 - 1.72: 2 1.72 - 1.85: 82 Bond restraints: 10909 Sorted by residual: bond pdb=" CB LEU A 20 " pdb=" CG LEU A 20 " ideal model delta sigma weight residual 1.530 1.605 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C6 MAN D 6 " pdb=" O6 MAN D 6 " ideal model delta sigma weight residual 1.407 1.479 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " ideal model delta sigma weight residual 1.526 1.455 0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C6 BMA D 3 " pdb=" O6 BMA D 3 " ideal model delta sigma weight residual 1.411 1.482 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C3 BMA D 3 " pdb=" O3 BMA D 3 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 10904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.52: 14647 4.52 - 9.03: 206 9.03 - 13.55: 1 13.55 - 18.06: 0 18.06 - 22.58: 2 Bond angle restraints: 14856 Sorted by residual: angle pdb=" CD1 LEU B 74 " pdb=" CG LEU B 74 " pdb=" CD2 LEU B 74 " ideal model delta sigma weight residual 110.80 133.38 -22.58 2.20e+00 2.07e-01 1.05e+02 angle pdb=" C ASP C 56 " pdb=" N PRO C 57 " pdb=" CA PRO C 57 " ideal model delta sigma weight residual 119.66 126.38 -6.72 7.30e-01 1.88e+00 8.49e+01 angle pdb=" CD1 LEU A 20 " pdb=" CG LEU A 20 " pdb=" CD2 LEU A 20 " ideal model delta sigma weight residual 110.80 130.49 -19.69 2.20e+00 2.07e-01 8.01e+01 angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 126.01 -6.35 7.20e-01 1.93e+00 7.78e+01 angle pdb=" C PRO C 57 " pdb=" N PRO C 58 " pdb=" CA PRO C 58 " ideal model delta sigma weight residual 119.66 125.85 -6.19 7.30e-01 1.88e+00 7.20e+01 ... (remaining 14851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 6108 15.63 - 31.26: 180 31.26 - 46.89: 56 46.89 - 62.51: 31 62.51 - 78.14: 9 Dihedral angle restraints: 6384 sinusoidal: 2465 harmonic: 3919 Sorted by residual: dihedral pdb=" CB CYS A 278 " pdb=" SG CYS A 278 " pdb=" SG CYS A 335 " pdb=" CB CYS A 335 " ideal model delta sinusoidal sigma weight residual -86.00 -130.64 44.64 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CA CYS A 534 " pdb=" CB CYS A 534 " pdb=" SG CYS A 534 " pdb=" SG CYS A 587 " ideal model delta sinusoidal sigma weight residual -73.00 -2.44 -70.56 1 2.00e+01 2.50e-03 1.60e+01 dihedral pdb=" CA VAL C 201 " pdb=" C VAL C 201 " pdb=" N PRO C 202 " pdb=" CA PRO C 202 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 6381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1541 0.116 - 0.232: 180 0.232 - 0.349: 11 0.349 - 0.465: 2 0.465 - 0.581: 1 Chirality restraints: 1735 Sorted by residual: chirality pdb=" C1 MAN D 4 " pdb=" O3 BMA D 3 " pdb=" C2 MAN D 4 " pdb=" O5 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.66e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 2.09e+01 chirality pdb=" C1 MAN D 5 " pdb=" O2 MAN D 4 " pdb=" C2 MAN D 5 " pdb=" O5 MAN D 5 " both_signs ideal model delta sigma weight residual False 2.40 2.47 -0.07 2.00e-02 2.50e+03 1.16e+01 ... (remaining 1732 not shown) Planarity restraints: 1871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 435 " 0.052 2.00e-02 2.50e+03 5.18e-02 3.35e+01 pdb=" CG ASN A 435 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 435 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 435 " -0.076 2.00e-02 2.50e+03 pdb=" C1 NAG A 707 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 202 " 0.047 2.00e-02 2.50e+03 4.03e-02 2.03e+01 pdb=" C7 NAG B 202 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG B 202 " 0.039 2.00e-02 2.50e+03 pdb=" N2 NAG B 202 " -0.062 2.00e-02 2.50e+03 pdb=" O7 NAG B 202 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 303 " -0.039 2.00e-02 2.50e+03 3.25e-02 1.32e+01 pdb=" C7 NAG C 303 " 0.009 2.00e-02 2.50e+03 pdb=" C8 NAG C 303 " -0.031 2.00e-02 2.50e+03 pdb=" N2 NAG C 303 " 0.052 2.00e-02 2.50e+03 pdb=" O7 NAG C 303 " 0.009 2.00e-02 2.50e+03 ... (remaining 1868 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3359 2.83 - 3.34: 9602 3.34 - 3.86: 18180 3.86 - 4.38: 20646 4.38 - 4.90: 34181 Nonbonded interactions: 85968 Sorted by model distance: nonbonded pdb=" OG1 THR C 200 " pdb=" OE PCA H 1 " model vdw 2.307 3.040 nonbonded pdb=" O3 NAG B 202 " pdb=" O7 NAG B 202 " model vdw 2.361 3.040 nonbonded pdb=" OD1 ASN A 405 " pdb=" OG1 THR A 635 " model vdw 2.412 3.040 nonbonded pdb=" OD1 ASN B 53 " pdb=" O5 NAG B 202 " model vdw 2.416 3.040 nonbonded pdb=" O LEU B 114 " pdb=" OG SER B 117 " model vdw 2.433 3.040 ... (remaining 85963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.010 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 0.014 0.076 10939 Z= 0.744 Angle : 1.317 22.578 14930 Z= 0.868 Chirality : 0.074 0.581 1735 Planarity : 0.006 0.040 1862 Dihedral : 9.987 78.144 3828 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 2.40 % Favored : 97.31 % Rotamer: Outliers : 0.43 % Allowed : 1.03 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.22), residues: 1336 helix: -0.31 (0.25), residues: 336 sheet: 0.87 (0.29), residues: 307 loop : -0.05 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 101 TYR 0.037 0.005 TYR L 99 PHE 0.029 0.005 PHE L 101 TRP 0.036 0.006 TRP H 160 HIS 0.006 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.01346 / 0.74 (10909) covalent geometry : angle 1.30377 / 0.87 (14856) SS BOND : bond 0.02407 / 1.80 ( 16) SS BOND : angle 3.87487 / 2.02 ( 32) hydrogen bonds : bond 0.17846 / 12.60 ( 483) hydrogen bonds : angle 7.70787 / 5.43 ( 1263) link_ALPHA1-2 : bond 0.02988 / 1.57 ( 1) link_ALPHA1-2 : angle 1.79106 / 0.95 ( 3) link_ALPHA1-3 : bond 0.04766 / 2.51 ( 1) link_ALPHA1-3 : angle 1.58088 / 0.78 ( 3) link_ALPHA1-6 : bond 0.01580 / 0.83 ( 1) link_ALPHA1-6 : angle 2.19658 / 1.11 ( 3) link_BETA1-4 : bond 0.04139 / 2.06 ( 2) link_BETA1-4 : angle 2.48549 / 1.12 ( 6) link_NAG-ASN : bond 0.02766 / 1.48 ( 9) link_NAG-ASN : angle 1.96292 / 0.97 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 393 time to evaluate : 0.410 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: A 25 LEU cc_start: 0.8735 (tt) cc_final: 0.8476 (mp) REVERT: A 73 LYS cc_start: 0.9077 (pttt) cc_final: 0.8853 (ttpt) REVERT: A 137 MET cc_start: 0.8721 (tpt) cc_final: 0.8476 (tmm) REVERT: A 217 THR cc_start: 0.9416 (m) cc_final: 0.9054 (t) REVERT: A 283 LEU cc_start: 0.9224 (mt) cc_final: 0.8974 (mt) REVERT: A 286 GLU cc_start: 0.8477 (tt0) cc_final: 0.8257 (tm-30) REVERT: A 317 TRP cc_start: 0.9231 (t60) cc_final: 0.8607 (t60) REVERT: A 318 LEU cc_start: 0.9669 (mt) cc_final: 0.9264 (mt) REVERT: A 384 PRO cc_start: 0.8738 (Cg_endo) cc_final: 0.8311 (Cg_exo) REVERT: A 404 TYR cc_start: 0.8521 (t80) cc_final: 0.8318 (t80) REVERT: A 413 LEU cc_start: 0.9196 (mt) cc_final: 0.8803 (tp) REVERT: A 417 MET cc_start: 0.8654 (mtt) cc_final: 0.8027 (mmm) REVERT: A 466 LEU cc_start: 0.8762 (mt) cc_final: 0.8534 (tt) REVERT: A 537 ARG cc_start: 0.8321 (mmt-90) cc_final: 0.8083 (mtt180) REVERT: A 551 THR cc_start: 0.9436 (m) cc_final: 0.8891 (p) REVERT: A 582 VAL cc_start: 0.9275 (t) cc_final: 0.8977 (t) REVERT: A 614 PHE cc_start: 0.8703 (m-80) cc_final: 0.8141 (m-80) REVERT: B 81 ASN cc_start: 0.8692 (t0) cc_final: 0.7772 (p0) REVERT: B 84 ASN cc_start: 0.9456 (m-40) cc_final: 0.9100 (m-40) REVERT: B 89 PHE cc_start: 0.9082 (m-80) cc_final: 0.8544 (m-80) REVERT: B 106 GLU cc_start: 0.9335 (tt0) cc_final: 0.8836 (tm-30) REVERT: B 115 TYR cc_start: 0.7975 (t80) cc_final: 0.7448 (t80) REVERT: B 128 LEU cc_start: 0.8441 (mt) cc_final: 0.8127 (mm) REVERT: C 81 TRP cc_start: 0.8456 (m-90) cc_final: 0.8210 (m100) REVERT: C 98 ASN cc_start: 0.0921 (OUTLIER) cc_final: -0.0613 (t0) REVERT: C 116 PHE cc_start: 0.8122 (m-80) cc_final: 0.7467 (m-80) REVERT: C 155 ASN cc_start: 0.7223 (m-40) cc_final: 0.7002 (m-40) REVERT: C 169 VAL cc_start: 0.7855 (t) cc_final: 0.7646 (p) REVERT: C 171 GLU cc_start: 0.8326 (mm-30) cc_final: 0.6783 (tm-30) REVERT: C 182 PHE cc_start: 0.7768 (m-80) cc_final: 0.7554 (m-80) REVERT: C 188 PHE cc_start: 0.8755 (m-80) cc_final: 0.8509 (m-80) REVERT: C 211 LEU cc_start: 0.9069 (mt) cc_final: 0.8585 (mm) REVERT: H 25 SER cc_start: 0.7949 (t) cc_final: 0.7677 (m) REVERT: H 32 PHE cc_start: 0.8798 (m-80) cc_final: 0.8303 (m-80) REVERT: H 69 MET cc_start: 0.7626 (mtm) cc_final: 0.6946 (mtm) REVERT: H 98 MET cc_start: 0.8100 (ttt) cc_final: 0.5716 (tpt) REVERT: H 160 TRP cc_start: 0.8302 (m100) cc_final: 0.7948 (m100) REVERT: H 165 LEU cc_start: 0.8342 (tp) cc_final: 0.7845 (mm) REVERT: H 215 LYS cc_start: 0.7945 (tppt) cc_final: 0.7733 (tptp) REVERT: L 3 GLU cc_start: 0.8691 (tt0) cc_final: 0.8275 (tm-30) REVERT: L 4 LEU cc_start: 0.8856 (mt) cc_final: 0.8630 (tt) REVERT: L 20 ILE cc_start: 0.9481 (mm) cc_final: 0.9275 (tp) REVERT: L 49 TYR cc_start: 0.8794 (m-80) cc_final: 0.7943 (m-80) REVERT: L 75 SER cc_start: 0.8572 (t) cc_final: 0.7781 (m) REVERT: L 84 ASP cc_start: 0.8821 (m-30) cc_final: 0.8545 (m-30) REVERT: L 99 TYR cc_start: 0.7893 (m-80) cc_final: 0.7300 (m-80) REVERT: L 121 LEU cc_start: 0.8511 (tp) cc_final: 0.8203 (tt) REVERT: L 136 LEU cc_start: 0.8919 (mt) cc_final: 0.8570 (mm) REVERT: L 138 CYS cc_start: 0.7638 (t) cc_final: 0.6899 (t) REVERT: L 143 PHE cc_start: 0.8874 (p90) cc_final: 0.8357 (p90) REVERT: L 174 ASN cc_start: 0.8797 (t0) cc_final: 0.8476 (t0) outliers start: 5 outliers final: 1 residues processed: 398 average time/residue: 0.1060 time to fit residues: 59.7563 Evaluate side-chains 236 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN L 88 GLN L 96 HIS L 192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.071937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.056674 restraints weight = 45433.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.058790 restraints weight = 25701.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.060233 restraints weight = 16989.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.061210 restraints weight = 12561.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.061882 restraints weight = 10095.053| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10939 Z= 0.160 Angle : 0.694 10.629 14930 Z= 0.359 Chirality : 0.045 0.354 1735 Planarity : 0.005 0.042 1862 Dihedral : 4.542 27.223 1459 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.22), residues: 1336 helix: 0.66 (0.27), residues: 343 sheet: 0.92 (0.28), residues: 327 loop : 0.06 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 418 TYR 0.026 0.002 TYR C 185 PHE 0.024 0.002 PHE L 101 TRP 0.015 0.002 TRP H 36 HIS 0.007 0.001 HIS H 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (10909) covalent geometry : angle 0.67192 / 0.35 (14856) SS BOND : bond 0.00379 / 0.26 ( 16) SS BOND : angle 1.19512 / 0.65 ( 32) hydrogen bonds : bond 0.05881 / 4.22 ( 483) hydrogen bonds : angle 5.82892 / 4.15 ( 1263) link_ALPHA1-2 : bond 0.00447 / 0.24 ( 1) link_ALPHA1-2 : angle 1.50271 / 0.68 ( 3) link_ALPHA1-3 : bond 0.00827 / 0.44 ( 1) link_ALPHA1-3 : angle 1.50169 / 0.81 ( 3) link_ALPHA1-6 : bond 0.00936 / 0.49 ( 1) link_ALPHA1-6 : angle 1.43392 / 0.60 ( 3) link_BETA1-4 : bond 0.02140 / 1.02 ( 2) link_BETA1-4 : angle 3.35914 / 1.50 ( 6) link_NAG-ASN : bond 0.00924 / 0.43 ( 9) link_NAG-ASN : angle 3.63237 / 2.32 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.411 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: A 126 LEU cc_start: 0.9361 (tp) cc_final: 0.9141 (tp) REVERT: A 137 MET cc_start: 0.8325 (tpt) cc_final: 0.7957 (tpp) REVERT: A 138 LEU cc_start: 0.9283 (mt) cc_final: 0.8698 (mt) REVERT: A 217 THR cc_start: 0.9353 (m) cc_final: 0.9072 (t) REVERT: A 283 LEU cc_start: 0.8951 (mt) cc_final: 0.8621 (mt) REVERT: A 317 TRP cc_start: 0.8976 (t60) cc_final: 0.8347 (t60) REVERT: A 318 LEU cc_start: 0.9523 (mt) cc_final: 0.9172 (mt) REVERT: A 349 GLU cc_start: 0.9275 (tt0) cc_final: 0.8951 (tt0) REVERT: A 413 LEU cc_start: 0.8822 (mt) cc_final: 0.8558 (tp) REVERT: A 417 MET cc_start: 0.8348 (mtt) cc_final: 0.7972 (mmm) REVERT: A 458 GLU cc_start: 0.8449 (tt0) cc_final: 0.7419 (tt0) REVERT: A 537 ARG cc_start: 0.8182 (mmt-90) cc_final: 0.7943 (mtt180) REVERT: A 551 THR cc_start: 0.9381 (m) cc_final: 0.8928 (p) REVERT: A 582 VAL cc_start: 0.9165 (t) cc_final: 0.8826 (t) REVERT: A 614 PHE cc_start: 0.8590 (m-80) cc_final: 0.8238 (m-80) REVERT: A 635 THR cc_start: 0.9202 (p) cc_final: 0.8891 (t) REVERT: A 649 PHE cc_start: 0.8292 (m-80) cc_final: 0.7974 (m-80) REVERT: B 81 ASN cc_start: 0.8804 (t0) cc_final: 0.8430 (t0) REVERT: B 84 ASN cc_start: 0.9288 (m-40) cc_final: 0.8998 (m-40) REVERT: B 89 PHE cc_start: 0.9029 (m-80) cc_final: 0.8120 (m-80) REVERT: B 106 GLU cc_start: 0.9232 (tt0) cc_final: 0.8747 (tm-30) REVERT: B 112 GLU cc_start: 0.9201 (pt0) cc_final: 0.8869 (pt0) REVERT: B 128 LEU cc_start: 0.8339 (mt) cc_final: 0.7969 (mm) REVERT: C 73 ASP cc_start: 0.6602 (t0) cc_final: 0.5866 (t0) REVERT: C 81 TRP cc_start: 0.8408 (m-90) cc_final: 0.8051 (m100) REVERT: C 116 PHE cc_start: 0.8213 (m-80) cc_final: 0.7241 (m-80) REVERT: C 171 GLU cc_start: 0.8079 (mm-30) cc_final: 0.6696 (tm-30) REVERT: C 182 PHE cc_start: 0.7858 (m-80) cc_final: 0.7345 (m-80) REVERT: C 198 PHE cc_start: 0.8874 (m-10) cc_final: 0.8611 (m-10) REVERT: H 32 PHE cc_start: 0.8612 (m-80) cc_final: 0.7822 (m-80) REVERT: H 97 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6743 (tm-30) REVERT: H 98 MET cc_start: 0.6366 (ttt) cc_final: 0.5817 (tpt) REVERT: H 101 ARG cc_start: 0.8418 (ptp-170) cc_final: 0.8028 (ptp-170) REVERT: L 3 GLU cc_start: 0.8577 (tt0) cc_final: 0.8212 (tm-30) REVERT: L 4 LEU cc_start: 0.8772 (mt) cc_final: 0.8525 (tp) REVERT: L 20 ILE cc_start: 0.9340 (mm) cc_final: 0.9054 (pt) REVERT: L 46 VAL cc_start: 0.9460 (m) cc_final: 0.9229 (p) REVERT: L 57 ILE cc_start: 0.7612 (mp) cc_final: 0.7145 (mp) REVERT: L 84 ASP cc_start: 0.8939 (m-30) cc_final: 0.8582 (m-30) REVERT: L 99 TYR cc_start: 0.7737 (m-80) cc_final: 0.6827 (m-80) REVERT: L 128 GLU cc_start: 0.9274 (tp30) cc_final: 0.8765 (tp30) REVERT: L 136 LEU cc_start: 0.8825 (mt) cc_final: 0.8515 (mm) REVERT: L 143 PHE cc_start: 0.8869 (p90) cc_final: 0.8289 (p90) REVERT: L 174 ASN cc_start: 0.8581 (t0) cc_final: 0.8149 (t0) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.0881 time to fit residues: 38.9055 Evaluate side-chains 212 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 96 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 HIS C 103 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.070237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.055071 restraints weight = 46794.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.057142 restraints weight = 26023.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.058565 restraints weight = 17025.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.059441 restraints weight = 12462.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.060147 restraints weight = 10068.767| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10939 Z= 0.155 Angle : 0.654 10.667 14930 Z= 0.338 Chirality : 0.045 0.270 1735 Planarity : 0.005 0.054 1862 Dihedral : 4.581 25.362 1459 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1336 helix: 0.70 (0.27), residues: 344 sheet: 0.77 (0.28), residues: 322 loop : 0.03 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 17 TYR 0.023 0.002 TYR C 185 PHE 0.035 0.002 PHE L 122 TRP 0.017 0.002 TRP L 189 HIS 0.006 0.001 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (10909) covalent geometry : angle 0.63558 / 0.33 (14856) SS BOND : bond 0.00372 / 0.24 ( 16) SS BOND : angle 1.13666 / 0.61 ( 32) hydrogen bonds : bond 0.05088 / 3.65 ( 483) hydrogen bonds : angle 5.50791 / 3.90 ( 1263) link_ALPHA1-2 : bond 0.00287 / 0.15 ( 1) link_ALPHA1-2 : angle 1.54490 / 0.81 ( 3) link_ALPHA1-3 : bond 0.00319 / 0.17 ( 1) link_ALPHA1-3 : angle 1.55193 / 0.73 ( 3) link_ALPHA1-6 : bond 0.00844 / 0.44 ( 1) link_ALPHA1-6 : angle 1.16426 / 0.61 ( 3) link_BETA1-4 : bond 0.01988 / 0.95 ( 2) link_BETA1-4 : angle 3.22409 / 1.43 ( 6) link_NAG-ASN : bond 0.00654 / 0.31 ( 9) link_NAG-ASN : angle 3.09307 / 2.08 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.316 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: A 137 MET cc_start: 0.8335 (tpt) cc_final: 0.8049 (tpp) REVERT: A 138 LEU cc_start: 0.9324 (mt) cc_final: 0.8777 (mt) REVERT: A 160 LEU cc_start: 0.8550 (pt) cc_final: 0.8016 (tp) REVERT: A 217 THR cc_start: 0.9306 (m) cc_final: 0.9088 (t) REVERT: A 256 MET cc_start: 0.9016 (tpp) cc_final: 0.8384 (tpp) REVERT: A 283 LEU cc_start: 0.9010 (mt) cc_final: 0.8442 (mt) REVERT: A 317 TRP cc_start: 0.9000 (t60) cc_final: 0.8436 (t60) REVERT: A 318 LEU cc_start: 0.9672 (mt) cc_final: 0.9275 (mt) REVERT: A 349 GLU cc_start: 0.9186 (tt0) cc_final: 0.8863 (tt0) REVERT: A 417 MET cc_start: 0.8546 (mtt) cc_final: 0.8132 (mmm) REVERT: A 451 THR cc_start: 0.9491 (m) cc_final: 0.9281 (p) REVERT: A 458 GLU cc_start: 0.8609 (tt0) cc_final: 0.7553 (tt0) REVERT: A 482 LEU cc_start: 0.9253 (mt) cc_final: 0.9024 (mt) REVERT: A 537 ARG cc_start: 0.8185 (mmt-90) cc_final: 0.7919 (mtt180) REVERT: A 551 THR cc_start: 0.9381 (m) cc_final: 0.8949 (p) REVERT: A 614 PHE cc_start: 0.8736 (m-80) cc_final: 0.8423 (m-10) REVERT: A 649 PHE cc_start: 0.8513 (m-80) cc_final: 0.8256 (m-80) REVERT: B 89 PHE cc_start: 0.8974 (m-80) cc_final: 0.8181 (m-80) REVERT: B 106 GLU cc_start: 0.9351 (tt0) cc_final: 0.8757 (tm-30) REVERT: B 112 GLU cc_start: 0.9236 (pt0) cc_final: 0.8953 (pt0) REVERT: B 128 LEU cc_start: 0.8451 (mt) cc_final: 0.8194 (mm) REVERT: C 73 ASP cc_start: 0.6114 (t0) cc_final: 0.5865 (t0) REVERT: C 81 TRP cc_start: 0.8636 (m-90) cc_final: 0.8147 (m100) REVERT: C 92 GLN cc_start: 0.8829 (mm110) cc_final: 0.8610 (mm110) REVERT: C 116 PHE cc_start: 0.8096 (m-80) cc_final: 0.7233 (m-80) REVERT: C 182 PHE cc_start: 0.8067 (m-80) cc_final: 0.7469 (m-80) REVERT: C 198 PHE cc_start: 0.8882 (m-10) cc_final: 0.8645 (m-10) REVERT: H 20 VAL cc_start: 0.9410 (t) cc_final: 0.9191 (t) REVERT: H 34 ILE cc_start: 0.8109 (mt) cc_final: 0.7887 (mt) REVERT: H 48 MET cc_start: 0.9376 (mtm) cc_final: 0.8461 (mpp) REVERT: H 98 MET cc_start: 0.6571 (ttt) cc_final: 0.6103 (tpt) REVERT: H 101 ARG cc_start: 0.8778 (ptp-170) cc_final: 0.8341 (ptp-170) REVERT: H 109 TRP cc_start: 0.8555 (m100) cc_final: 0.7525 (m-10) REVERT: H 215 LYS cc_start: 0.8124 (tppt) cc_final: 0.7686 (tptp) REVERT: L 3 GLU cc_start: 0.8650 (tt0) cc_final: 0.8290 (tm-30) REVERT: L 4 LEU cc_start: 0.8765 (mt) cc_final: 0.8525 (tp) REVERT: L 20 ILE cc_start: 0.9364 (mm) cc_final: 0.9100 (pt) REVERT: L 46 VAL cc_start: 0.9379 (m) cc_final: 0.9162 (p) REVERT: L 84 ASP cc_start: 0.8972 (m-30) cc_final: 0.8764 (m-30) REVERT: L 99 TYR cc_start: 0.8148 (m-80) cc_final: 0.7367 (m-80) REVERT: L 136 LEU cc_start: 0.8800 (mt) cc_final: 0.8489 (mm) REVERT: L 143 PHE cc_start: 0.9030 (p90) cc_final: 0.8226 (p90) REVERT: L 174 ASN cc_start: 0.8729 (t0) cc_final: 0.8348 (t0) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.0859 time to fit residues: 33.2436 Evaluate side-chains 200 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 22 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 HIS ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN C 92 GLN L 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.052668 restraints weight = 47376.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.054618 restraints weight = 26754.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.055861 restraints weight = 17729.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.056819 restraints weight = 13371.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.057420 restraints weight = 10714.602| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 10939 Z= 0.190 Angle : 0.673 10.408 14930 Z= 0.343 Chirality : 0.044 0.243 1735 Planarity : 0.005 0.044 1862 Dihedral : 4.780 29.901 1459 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.22), residues: 1336 helix: 0.87 (0.27), residues: 333 sheet: 0.60 (0.27), residues: 331 loop : 0.07 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 17 TYR 0.017 0.002 TYR C 117 PHE 0.022 0.002 PHE A 250 TRP 0.023 0.003 TRP H 160 HIS 0.009 0.002 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (10909) covalent geometry : angle 0.64718 / 0.34 (14856) SS BOND : bond 0.00381 / 0.24 ( 16) SS BOND : angle 1.07166 / 0.64 ( 32) hydrogen bonds : bond 0.04802 / 3.43 ( 483) hydrogen bonds : angle 5.48078 / 3.89 ( 1263) link_ALPHA1-2 : bond 0.00233 / 0.12 ( 1) link_ALPHA1-2 : angle 1.77982 / 0.96 ( 3) link_ALPHA1-3 : bond 0.00015 / 0.01 ( 1) link_ALPHA1-3 : angle 1.86336 / 0.90 ( 3) link_ALPHA1-6 : bond 0.00916 / 0.48 ( 1) link_ALPHA1-6 : angle 1.15917 / 0.64 ( 3) link_BETA1-4 : bond 0.02091 / 1.00 ( 2) link_BETA1-4 : angle 3.26992 / 1.46 ( 6) link_NAG-ASN : bond 0.00731 / 0.35 ( 9) link_NAG-ASN : angle 3.88735 / 2.41 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.337 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: A 121 MET cc_start: 0.8622 (mtt) cc_final: 0.8338 (mmm) REVERT: A 160 LEU cc_start: 0.8540 (pt) cc_final: 0.8085 (tp) REVERT: A 217 THR cc_start: 0.9378 (m) cc_final: 0.9112 (t) REVERT: A 317 TRP cc_start: 0.9111 (t60) cc_final: 0.8583 (t60) REVERT: A 318 LEU cc_start: 0.9642 (mt) cc_final: 0.9342 (mt) REVERT: A 349 GLU cc_start: 0.9232 (tt0) cc_final: 0.8763 (tt0) REVERT: A 364 LEU cc_start: 0.9490 (tt) cc_final: 0.9287 (tt) REVERT: A 458 GLU cc_start: 0.8492 (tt0) cc_final: 0.7664 (tt0) REVERT: A 544 ILE cc_start: 0.9173 (mt) cc_final: 0.8888 (mt) REVERT: A 551 THR cc_start: 0.9430 (m) cc_final: 0.9074 (p) REVERT: A 614 PHE cc_start: 0.8810 (m-80) cc_final: 0.8263 (m-80) REVERT: A 649 PHE cc_start: 0.8435 (m-80) cc_final: 0.8109 (m-80) REVERT: B 81 ASN cc_start: 0.8761 (t0) cc_final: 0.8500 (t0) REVERT: B 89 PHE cc_start: 0.9003 (m-80) cc_final: 0.8220 (m-80) REVERT: B 106 GLU cc_start: 0.9355 (tt0) cc_final: 0.8774 (tm-30) REVERT: B 107 LEU cc_start: 0.9573 (tp) cc_final: 0.9361 (tp) REVERT: B 128 LEU cc_start: 0.8400 (mt) cc_final: 0.8040 (mm) REVERT: C 81 TRP cc_start: 0.8856 (m-90) cc_final: 0.8032 (m100) REVERT: C 105 ARG cc_start: 0.9362 (tpp80) cc_final: 0.9040 (tpp80) REVERT: C 182 PHE cc_start: 0.8031 (m-80) cc_final: 0.7507 (m-80) REVERT: C 198 PHE cc_start: 0.9010 (m-10) cc_final: 0.8734 (m-10) REVERT: H 48 MET cc_start: 0.9329 (mtm) cc_final: 0.8178 (mtp) REVERT: H 80 MET cc_start: 0.9178 (ttp) cc_final: 0.8907 (ttm) REVERT: H 98 MET cc_start: 0.6882 (ttt) cc_final: 0.6462 (tpt) REVERT: H 212 LYS cc_start: 0.9067 (tttp) cc_final: 0.8026 (mmtt) REVERT: H 215 LYS cc_start: 0.8407 (tppt) cc_final: 0.7996 (tptp) REVERT: L 3 GLU cc_start: 0.8638 (tt0) cc_final: 0.8298 (tm-30) REVERT: L 4 LEU cc_start: 0.8735 (mt) cc_final: 0.8387 (tt) REVERT: L 46 VAL cc_start: 0.9400 (m) cc_final: 0.9132 (p) REVERT: L 81 ASP cc_start: 0.8474 (m-30) cc_final: 0.7983 (m-30) REVERT: L 84 ASP cc_start: 0.8981 (m-30) cc_final: 0.8716 (m-30) REVERT: L 99 TYR cc_start: 0.8453 (m-80) cc_final: 0.5986 (m-10) REVERT: L 136 LEU cc_start: 0.8732 (mt) cc_final: 0.8445 (mm) REVERT: L 143 PHE cc_start: 0.9067 (p90) cc_final: 0.8226 (p90) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.0843 time to fit residues: 31.0377 Evaluate side-chains 182 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.6980 chunk 75 optimal weight: 20.0000 chunk 127 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 26 HIS ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS H 54 ASN H 170 HIS L 192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.065606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.050006 restraints weight = 49156.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.051822 restraints weight = 28380.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.053074 restraints weight = 19112.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.053925 restraints weight = 14360.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.054456 restraints weight = 11725.938| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10939 Z= 0.253 Angle : 0.748 10.051 14930 Z= 0.382 Chirality : 0.045 0.213 1735 Planarity : 0.006 0.061 1862 Dihedral : 5.127 32.530 1459 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.22), residues: 1336 helix: 0.54 (0.27), residues: 340 sheet: 0.58 (0.27), residues: 312 loop : -0.31 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 71 TYR 0.028 0.002 TYR L 144 PHE 0.027 0.003 PHE B 88 TRP 0.016 0.002 TRP L 34 HIS 0.012 0.002 HIS A 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.25 (10909) covalent geometry : angle 0.73025 / 0.38 (14856) SS BOND : bond 0.00477 / 0.32 ( 16) SS BOND : angle 1.20498 / 0.72 ( 32) hydrogen bonds : bond 0.05085 / 3.63 ( 483) hydrogen bonds : angle 5.80319 / 4.10 ( 1263) link_ALPHA1-2 : bond 0.00198 / 0.10 ( 1) link_ALPHA1-2 : angle 2.16565 / 1.22 ( 3) link_ALPHA1-3 : bond 0.00260 / 0.14 ( 1) link_ALPHA1-3 : angle 2.26234 / 1.11 ( 3) link_ALPHA1-6 : bond 0.00948 / 0.50 ( 1) link_ALPHA1-6 : angle 1.18699 / 0.69 ( 3) link_BETA1-4 : bond 0.02173 / 1.04 ( 2) link_BETA1-4 : angle 3.57427 / 1.61 ( 6) link_NAG-ASN : bond 0.00694 / 0.37 ( 9) link_NAG-ASN : angle 3.13844 / 2.10 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.408 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: A 121 MET cc_start: 0.8877 (mtt) cc_final: 0.8336 (mmm) REVERT: A 138 LEU cc_start: 0.9291 (mt) cc_final: 0.8828 (mt) REVERT: A 160 LEU cc_start: 0.8718 (pt) cc_final: 0.8118 (tp) REVERT: A 283 LEU cc_start: 0.8904 (mt) cc_final: 0.8695 (mt) REVERT: A 317 TRP cc_start: 0.9255 (t60) cc_final: 0.8622 (t60) REVERT: A 318 LEU cc_start: 0.9707 (mt) cc_final: 0.9318 (mt) REVERT: A 349 GLU cc_start: 0.9361 (tt0) cc_final: 0.8987 (tt0) REVERT: A 458 GLU cc_start: 0.8508 (tt0) cc_final: 0.7524 (tt0) REVERT: A 494 MET cc_start: 0.8378 (ttm) cc_final: 0.8175 (ttm) REVERT: A 544 ILE cc_start: 0.9183 (mt) cc_final: 0.8879 (mt) REVERT: B 47 ASP cc_start: 0.9149 (m-30) cc_final: 0.8863 (m-30) REVERT: B 88 PHE cc_start: 0.9353 (t80) cc_final: 0.8861 (t80) REVERT: B 89 PHE cc_start: 0.9185 (m-80) cc_final: 0.8512 (m-80) REVERT: B 106 GLU cc_start: 0.9332 (tt0) cc_final: 0.8704 (tm-30) REVERT: B 107 LEU cc_start: 0.9560 (tp) cc_final: 0.9327 (tp) REVERT: C 81 TRP cc_start: 0.8962 (m-90) cc_final: 0.8012 (m100) REVERT: C 105 ARG cc_start: 0.9386 (tpp80) cc_final: 0.9051 (tpp80) REVERT: C 171 GLU cc_start: 0.8030 (mm-30) cc_final: 0.6943 (tm-30) REVERT: C 198 PHE cc_start: 0.8943 (m-10) cc_final: 0.8710 (m-10) REVERT: H 46 GLU cc_start: 0.8520 (tt0) cc_final: 0.7957 (tp30) REVERT: H 48 MET cc_start: 0.9337 (mtm) cc_final: 0.8401 (mtp) REVERT: H 104 PHE cc_start: 0.9163 (m-80) cc_final: 0.8556 (m-10) REVERT: H 212 LYS cc_start: 0.9218 (tttp) cc_final: 0.8385 (mmtt) REVERT: H 215 LYS cc_start: 0.8399 (tppt) cc_final: 0.8127 (ttpt) REVERT: L 3 GLU cc_start: 0.8775 (tt0) cc_final: 0.8465 (tm-30) REVERT: L 4 LEU cc_start: 0.8817 (mt) cc_final: 0.8468 (mm) REVERT: L 36 GLN cc_start: 0.8969 (pp30) cc_final: 0.8506 (pp30) REVERT: L 99 TYR cc_start: 0.8551 (m-80) cc_final: 0.7313 (m-10) REVERT: L 136 LEU cc_start: 0.8530 (mt) cc_final: 0.8036 (mm) REVERT: L 140 ILE cc_start: 0.9476 (mp) cc_final: 0.9208 (mp) REVERT: L 143 PHE cc_start: 0.9013 (p90) cc_final: 0.8159 (p90) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.0818 time to fit residues: 28.6249 Evaluate side-chains 172 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 14 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 chunk 69 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS C 103 ASN L 25 HIS L 31 ASN ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 192 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.068058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.052586 restraints weight = 48131.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.054550 restraints weight = 27311.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.055892 restraints weight = 18105.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.056813 restraints weight = 13371.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.057425 restraints weight = 10769.058| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10939 Z= 0.137 Angle : 0.646 10.216 14930 Z= 0.326 Chirality : 0.044 0.242 1735 Planarity : 0.005 0.044 1862 Dihedral : 4.792 28.256 1459 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.09 % Allowed : 1.46 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.23), residues: 1336 helix: 0.85 (0.27), residues: 337 sheet: 0.57 (0.27), residues: 321 loop : -0.05 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 418 TYR 0.012 0.002 TYR L 195 PHE 0.022 0.002 PHE A 238 TRP 0.029 0.002 TRP H 160 HIS 0.004 0.001 HIS A 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (10909) covalent geometry : angle 0.62599 / 0.32 (14856) SS BOND : bond 0.00285 / 0.20 ( 16) SS BOND : angle 1.25771 / 0.70 ( 32) hydrogen bonds : bond 0.04471 / 3.19 ( 483) hydrogen bonds : angle 5.45583 / 3.87 ( 1263) link_ALPHA1-2 : bond 0.00358 / 0.19 ( 1) link_ALPHA1-2 : angle 1.83200 / 0.99 ( 3) link_ALPHA1-3 : bond 0.00029 / 0.02 ( 1) link_ALPHA1-3 : angle 1.84012 / 0.87 ( 3) link_ALPHA1-6 : bond 0.00778 / 0.41 ( 1) link_ALPHA1-6 : angle 1.28736 / 0.61 ( 3) link_BETA1-4 : bond 0.01918 / 0.91 ( 2) link_BETA1-4 : angle 3.08892 / 1.38 ( 6) link_NAG-ASN : bond 0.00703 / 0.30 ( 9) link_NAG-ASN : angle 3.19713 / 2.13 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.272 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: A 68 MET cc_start: 0.8578 (tpp) cc_final: 0.8357 (mmm) REVERT: A 121 MET cc_start: 0.8770 (mtt) cc_final: 0.8380 (mmm) REVERT: A 138 LEU cc_start: 0.9342 (mt) cc_final: 0.9139 (mt) REVERT: A 160 LEU cc_start: 0.8625 (pt) cc_final: 0.8260 (tp) REVERT: A 163 ASN cc_start: 0.8371 (m110) cc_final: 0.8091 (m-40) REVERT: A 317 TRP cc_start: 0.9156 (t60) cc_final: 0.8662 (t60) REVERT: A 318 LEU cc_start: 0.9687 (mt) cc_final: 0.9451 (mt) REVERT: A 349 GLU cc_start: 0.9311 (tt0) cc_final: 0.8707 (tt0) REVERT: A 356 MET cc_start: 0.8560 (tpp) cc_final: 0.8300 (tpp) REVERT: A 458 GLU cc_start: 0.8695 (tt0) cc_final: 0.7927 (tt0) REVERT: A 543 MET cc_start: 0.7713 (tpp) cc_final: 0.7422 (tpp) REVERT: A 544 ILE cc_start: 0.9265 (mt) cc_final: 0.9001 (mt) REVERT: B 81 ASN cc_start: 0.8587 (t0) cc_final: 0.7531 (t0) REVERT: B 88 PHE cc_start: 0.9270 (t80) cc_final: 0.8950 (t80) REVERT: B 106 GLU cc_start: 0.9292 (tt0) cc_final: 0.8659 (tm-30) REVERT: B 107 LEU cc_start: 0.9526 (tp) cc_final: 0.9246 (tp) REVERT: C 73 ASP cc_start: 0.8240 (t0) cc_final: 0.7893 (t0) REVERT: C 81 TRP cc_start: 0.8837 (m-90) cc_final: 0.7876 (m100) REVERT: C 92 GLN cc_start: 0.9077 (mm110) cc_final: 0.8791 (mm110) REVERT: C 105 ARG cc_start: 0.9375 (tpp80) cc_final: 0.9029 (tpp80) REVERT: C 106 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8250 (mt-10) REVERT: C 171 GLU cc_start: 0.7942 (mm-30) cc_final: 0.6910 (tm-30) REVERT: H 46 GLU cc_start: 0.8507 (tt0) cc_final: 0.8020 (tp30) REVERT: H 48 MET cc_start: 0.9432 (mtm) cc_final: 0.8336 (mtp) REVERT: H 146 CYS cc_start: 0.3934 (p) cc_final: 0.3423 (p) REVERT: H 212 LYS cc_start: 0.9177 (tttm) cc_final: 0.8508 (mmtt) REVERT: H 215 LYS cc_start: 0.8214 (tppt) cc_final: 0.7803 (tptp) REVERT: L 3 GLU cc_start: 0.8795 (tt0) cc_final: 0.8312 (tm-30) REVERT: L 4 LEU cc_start: 0.8792 (mt) cc_final: 0.8295 (tp) REVERT: L 86 TYR cc_start: 0.8466 (m-80) cc_final: 0.7991 (m-80) REVERT: L 99 TYR cc_start: 0.7552 (m-80) cc_final: 0.6198 (m-80) REVERT: L 136 LEU cc_start: 0.8385 (mt) cc_final: 0.8048 (mm) REVERT: L 140 ILE cc_start: 0.9453 (mp) cc_final: 0.9171 (mp) REVERT: L 143 PHE cc_start: 0.9013 (p90) cc_final: 0.8170 (p90) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.0876 time to fit residues: 30.8510 Evaluate side-chains 174 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 0.0040 chunk 98 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS L 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.066744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.051527 restraints weight = 48078.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.053372 restraints weight = 27394.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.054615 restraints weight = 18275.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.055515 restraints weight = 13633.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.056000 restraints weight = 11016.656| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10939 Z= 0.183 Angle : 0.673 11.527 14930 Z= 0.344 Chirality : 0.043 0.226 1735 Planarity : 0.005 0.044 1862 Dihedral : 4.850 21.817 1459 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.23), residues: 1336 helix: 0.87 (0.27), residues: 337 sheet: 0.53 (0.27), residues: 323 loop : -0.12 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 418 TYR 0.015 0.002 TYR B 115 PHE 0.025 0.002 PHE B 89 TRP 0.028 0.002 TRP L 189 HIS 0.008 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (10909) covalent geometry : angle 0.65406 / 0.34 (14856) SS BOND : bond 0.00463 / 0.31 ( 16) SS BOND : angle 1.26705 / 0.68 ( 32) hydrogen bonds : bond 0.04552 / 3.27 ( 483) hydrogen bonds : angle 5.59239 / 3.96 ( 1263) link_ALPHA1-2 : bond 0.00382 / 0.20 ( 1) link_ALPHA1-2 : angle 2.01095 / 1.11 ( 3) link_ALPHA1-3 : bond 0.00074 / 0.04 ( 1) link_ALPHA1-3 : angle 2.03475 / 0.98 ( 3) link_ALPHA1-6 : bond 0.00809 / 0.43 ( 1) link_ALPHA1-6 : angle 1.15002 / 0.62 ( 3) link_BETA1-4 : bond 0.02074 / 0.99 ( 2) link_BETA1-4 : angle 3.36231 / 1.51 ( 6) link_NAG-ASN : bond 0.00581 / 0.28 ( 9) link_NAG-ASN : angle 3.06857 / 2.08 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.424 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: A 160 LEU cc_start: 0.8828 (pt) cc_final: 0.8341 (tp) REVERT: A 317 TRP cc_start: 0.9249 (t60) cc_final: 0.8774 (t60) REVERT: A 318 LEU cc_start: 0.9691 (mt) cc_final: 0.9456 (mt) REVERT: A 349 GLU cc_start: 0.9382 (tt0) cc_final: 0.8961 (tt0) REVERT: A 356 MET cc_start: 0.8595 (tpp) cc_final: 0.8316 (tpp) REVERT: A 458 GLU cc_start: 0.8732 (tt0) cc_final: 0.8019 (tt0) REVERT: A 494 MET cc_start: 0.8454 (ttm) cc_final: 0.8211 (ttm) REVERT: A 543 MET cc_start: 0.7695 (tpp) cc_final: 0.7465 (tpp) REVERT: A 544 ILE cc_start: 0.9216 (mt) cc_final: 0.8987 (mt) REVERT: B 81 ASN cc_start: 0.8531 (t0) cc_final: 0.8103 (t0) REVERT: B 94 LYS cc_start: 0.9149 (tppt) cc_final: 0.8942 (tppt) REVERT: C 73 ASP cc_start: 0.8241 (t0) cc_final: 0.7811 (t0) REVERT: C 81 TRP cc_start: 0.8771 (m-90) cc_final: 0.7838 (m100) REVERT: C 105 ARG cc_start: 0.9331 (tpp80) cc_final: 0.9046 (tpp80) REVERT: C 125 TRP cc_start: 0.7875 (t60) cc_final: 0.7170 (t60) REVERT: C 171 GLU cc_start: 0.7982 (mm-30) cc_final: 0.6968 (tm-30) REVERT: H 46 GLU cc_start: 0.8553 (tt0) cc_final: 0.8035 (tp30) REVERT: H 48 MET cc_start: 0.9451 (mtm) cc_final: 0.8413 (mtp) REVERT: H 212 LYS cc_start: 0.9193 (tttm) cc_final: 0.8508 (mmtt) REVERT: H 215 LYS cc_start: 0.8106 (tppt) cc_final: 0.7591 (tptp) REVERT: L 3 GLU cc_start: 0.8743 (tt0) cc_final: 0.8209 (tm-30) REVERT: L 4 LEU cc_start: 0.8816 (mt) cc_final: 0.8320 (tp) REVERT: L 86 TYR cc_start: 0.8495 (m-80) cc_final: 0.8094 (m-80) REVERT: L 136 LEU cc_start: 0.8488 (mt) cc_final: 0.8044 (mm) REVERT: L 140 ILE cc_start: 0.9437 (mp) cc_final: 0.9159 (mp) REVERT: L 143 PHE cc_start: 0.9059 (p90) cc_final: 0.8229 (p90) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.0807 time to fit residues: 27.1409 Evaluate side-chains 166 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 41 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 7 optimal weight: 0.0000 chunk 16 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 HIS B 30 HIS ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN L 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.067331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.052177 restraints weight = 47974.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.054087 restraints weight = 27327.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.055379 restraints weight = 18085.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.056259 restraints weight = 13344.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.056798 restraints weight = 10742.493| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10939 Z= 0.159 Angle : 0.666 10.187 14930 Z= 0.339 Chirality : 0.044 0.259 1735 Planarity : 0.005 0.043 1862 Dihedral : 4.857 21.298 1459 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.09 % Allowed : 0.95 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.23), residues: 1336 helix: 0.83 (0.27), residues: 336 sheet: 0.59 (0.28), residues: 313 loop : -0.09 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 418 TYR 0.038 0.002 TYR L 49 PHE 0.028 0.002 PHE A 232 TRP 0.017 0.002 TRP H 160 HIS 0.005 0.001 HIS A 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (10909) covalent geometry : angle 0.64661 / 0.33 (14856) SS BOND : bond 0.00317 / 0.21 ( 16) SS BOND : angle 1.70144 / 1.04 ( 32) hydrogen bonds : bond 0.04481 / 3.20 ( 483) hydrogen bonds : angle 5.59365 / 3.97 ( 1263) link_ALPHA1-2 : bond 0.00403 / 0.21 ( 1) link_ALPHA1-2 : angle 1.93870 / 1.06 ( 3) link_ALPHA1-3 : bond 0.00025 / 0.01 ( 1) link_ALPHA1-3 : angle 1.93548 / 0.93 ( 3) link_ALPHA1-6 : bond 0.00811 / 0.43 ( 1) link_ALPHA1-6 : angle 1.20283 / 0.61 ( 3) link_BETA1-4 : bond 0.01967 / 0.94 ( 2) link_BETA1-4 : angle 3.22752 / 1.45 ( 6) link_NAG-ASN : bond 0.00571 / 0.27 ( 9) link_NAG-ASN : angle 2.97057 / 2.03 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 0.434 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: A 126 LEU cc_start: 0.9421 (tp) cc_final: 0.9210 (tp) REVERT: A 137 MET cc_start: 0.8321 (tmm) cc_final: 0.7949 (tmm) REVERT: A 138 LEU cc_start: 0.9039 (mt) cc_final: 0.8576 (mt) REVERT: A 160 LEU cc_start: 0.8679 (pt) cc_final: 0.8110 (tp) REVERT: A 163 ASN cc_start: 0.8248 (m110) cc_final: 0.7861 (m-40) REVERT: A 317 TRP cc_start: 0.9184 (t60) cc_final: 0.8722 (t60) REVERT: A 318 LEU cc_start: 0.9744 (mt) cc_final: 0.9463 (mt) REVERT: A 349 GLU cc_start: 0.9360 (tt0) cc_final: 0.8970 (tt0) REVERT: A 356 MET cc_start: 0.8642 (tpp) cc_final: 0.8354 (tpp) REVERT: A 458 GLU cc_start: 0.8715 (tt0) cc_final: 0.7982 (tt0) REVERT: A 543 MET cc_start: 0.7880 (tpp) cc_final: 0.7664 (tpp) REVERT: A 544 ILE cc_start: 0.9219 (mt) cc_final: 0.8996 (mt) REVERT: A 579 LEU cc_start: 0.9263 (tp) cc_final: 0.8341 (pp) REVERT: B 47 ASP cc_start: 0.9093 (m-30) cc_final: 0.8863 (m-30) REVERT: B 81 ASN cc_start: 0.8502 (t0) cc_final: 0.8207 (t0) REVERT: B 89 PHE cc_start: 0.9136 (m-80) cc_final: 0.8444 (m-80) REVERT: B 106 GLU cc_start: 0.9315 (tt0) cc_final: 0.8777 (pt0) REVERT: C 73 ASP cc_start: 0.8337 (t0) cc_final: 0.8040 (t0) REVERT: C 81 TRP cc_start: 0.8696 (m-90) cc_final: 0.7804 (m100) REVERT: C 105 ARG cc_start: 0.9331 (tpp80) cc_final: 0.9043 (tpp80) REVERT: C 125 TRP cc_start: 0.7896 (t60) cc_final: 0.7346 (t60) REVERT: C 171 GLU cc_start: 0.8014 (mm-30) cc_final: 0.6906 (tm-30) REVERT: H 46 GLU cc_start: 0.8516 (tt0) cc_final: 0.8010 (tp30) REVERT: H 48 MET cc_start: 0.9398 (mtm) cc_final: 0.8804 (mtt) REVERT: H 104 PHE cc_start: 0.8898 (m-80) cc_final: 0.8694 (m-10) REVERT: H 212 LYS cc_start: 0.9234 (tttm) cc_final: 0.8523 (mmtt) REVERT: H 215 LYS cc_start: 0.8041 (tppt) cc_final: 0.7514 (tptp) REVERT: L 3 GLU cc_start: 0.8769 (tt0) cc_final: 0.8233 (tm-30) REVERT: L 4 LEU cc_start: 0.8789 (mt) cc_final: 0.8209 (tp) REVERT: L 86 TYR cc_start: 0.8438 (m-80) cc_final: 0.8061 (m-80) REVERT: L 136 LEU cc_start: 0.8668 (mt) cc_final: 0.8320 (mm) REVERT: L 140 ILE cc_start: 0.9443 (mp) cc_final: 0.9125 (mp) REVERT: L 143 PHE cc_start: 0.9047 (p90) cc_final: 0.8247 (p90) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.0871 time to fit residues: 29.0854 Evaluate side-chains 170 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 92 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 84 optimal weight: 0.0020 chunk 48 optimal weight: 0.2980 chunk 129 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 HIS C 103 ASN H 205 ASN L 33 HIS ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.068466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.053151 restraints weight = 47530.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.055068 restraints weight = 27251.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056374 restraints weight = 18096.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.057267 restraints weight = 13395.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.057836 restraints weight = 10804.594| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10939 Z= 0.132 Angle : 0.661 12.111 14930 Z= 0.332 Chirality : 0.044 0.273 1735 Planarity : 0.005 0.043 1862 Dihedral : 4.755 28.473 1459 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.23), residues: 1336 helix: 0.83 (0.28), residues: 335 sheet: 0.68 (0.28), residues: 315 loop : -0.06 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 216 TYR 0.031 0.002 TYR L 49 PHE 0.019 0.002 PHE C 109 TRP 0.015 0.002 TRP H 36 HIS 0.011 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (10909) covalent geometry : angle 0.63752 / 0.33 (14856) SS BOND : bond 0.00414 / 0.24 ( 16) SS BOND : angle 1.24318 / 0.68 ( 32) hydrogen bonds : bond 0.04259 / 3.05 ( 483) hydrogen bonds : angle 5.48651 / 3.87 ( 1263) link_ALPHA1-2 : bond 0.00491 / 0.26 ( 1) link_ALPHA1-2 : angle 1.73918 / 0.94 ( 3) link_ALPHA1-3 : bond 0.00093 / 0.05 ( 1) link_ALPHA1-3 : angle 1.79490 / 0.86 ( 3) link_ALPHA1-6 : bond 0.00742 / 0.39 ( 1) link_ALPHA1-6 : angle 1.24436 / 0.60 ( 3) link_BETA1-4 : bond 0.01905 / 0.91 ( 2) link_BETA1-4 : angle 3.14294 / 1.41 ( 6) link_NAG-ASN : bond 0.00613 / 0.29 ( 9) link_NAG-ASN : angle 3.64366 / 2.18 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8235 (tmm) cc_final: 0.7820 (tmm) REVERT: A 138 LEU cc_start: 0.9047 (mt) cc_final: 0.8535 (mt) REVERT: A 160 LEU cc_start: 0.8646 (pt) cc_final: 0.8150 (tp) REVERT: A 163 ASN cc_start: 0.8370 (m110) cc_final: 0.8029 (m-40) REVERT: A 317 TRP cc_start: 0.9154 (t60) cc_final: 0.8740 (t60) REVERT: A 318 LEU cc_start: 0.9735 (mt) cc_final: 0.9439 (pp) REVERT: A 349 GLU cc_start: 0.9306 (tt0) cc_final: 0.8848 (tt0) REVERT: A 356 MET cc_start: 0.8561 (tpp) cc_final: 0.8276 (tpp) REVERT: A 458 GLU cc_start: 0.8538 (tt0) cc_final: 0.7783 (tt0) REVERT: A 482 LEU cc_start: 0.9342 (mt) cc_final: 0.9133 (mt) REVERT: A 544 ILE cc_start: 0.9260 (mt) cc_final: 0.9052 (mt) REVERT: A 579 LEU cc_start: 0.9189 (tp) cc_final: 0.8268 (pp) REVERT: B 47 ASP cc_start: 0.9081 (m-30) cc_final: 0.8871 (m-30) REVERT: B 81 ASN cc_start: 0.8558 (t0) cc_final: 0.8341 (t0) REVERT: B 89 PHE cc_start: 0.9059 (m-80) cc_final: 0.8244 (m-80) REVERT: B 93 LEU cc_start: 0.9535 (mt) cc_final: 0.9334 (mt) REVERT: B 100 LEU cc_start: 0.9180 (mt) cc_final: 0.8705 (mt) REVERT: B 106 GLU cc_start: 0.9283 (tt0) cc_final: 0.8761 (pt0) REVERT: C 73 ASP cc_start: 0.8319 (t0) cc_final: 0.8030 (t0) REVERT: C 81 TRP cc_start: 0.8659 (m-90) cc_final: 0.7746 (m100) REVERT: C 92 GLN cc_start: 0.9088 (mm110) cc_final: 0.8870 (mm110) REVERT: C 105 ARG cc_start: 0.9147 (tpp80) cc_final: 0.8885 (tpp80) REVERT: C 106 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8098 (mt-10) REVERT: C 125 TRP cc_start: 0.7740 (t60) cc_final: 0.7256 (t60) REVERT: H 46 GLU cc_start: 0.8482 (tt0) cc_final: 0.8076 (tp30) REVERT: H 48 MET cc_start: 0.9448 (mtm) cc_final: 0.8519 (mtp) REVERT: H 69 MET cc_start: 0.7392 (mmp) cc_final: 0.6817 (mmm) REVERT: H 160 TRP cc_start: 0.8242 (m100) cc_final: 0.8039 (m100) REVERT: H 212 LYS cc_start: 0.9210 (tttm) cc_final: 0.8572 (mptt) REVERT: H 215 LYS cc_start: 0.7902 (tppt) cc_final: 0.7441 (tptp) REVERT: L 3 GLU cc_start: 0.8700 (tt0) cc_final: 0.8170 (tm-30) REVERT: L 4 LEU cc_start: 0.8717 (mt) cc_final: 0.8132 (tp) REVERT: L 86 TYR cc_start: 0.8350 (m-80) cc_final: 0.7918 (m-80) REVERT: L 136 LEU cc_start: 0.8831 (mt) cc_final: 0.8550 (mm) REVERT: L 140 ILE cc_start: 0.9410 (mp) cc_final: 0.9120 (mp) REVERT: L 143 PHE cc_start: 0.9041 (p90) cc_final: 0.8214 (p90) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.0852 time to fit residues: 27.6297 Evaluate side-chains 167 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 41 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 655 HIS B 30 HIS ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.067475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.052007 restraints weight = 48348.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.053890 restraints weight = 27816.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.055176 restraints weight = 18613.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.056057 restraints weight = 13884.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.056615 restraints weight = 11270.275| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10939 Z= 0.161 Angle : 0.662 10.198 14930 Z= 0.336 Chirality : 0.043 0.283 1735 Planarity : 0.005 0.044 1862 Dihedral : 4.816 25.777 1459 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.23), residues: 1336 helix: 0.75 (0.27), residues: 336 sheet: 0.64 (0.28), residues: 310 loop : -0.08 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 216 TYR 0.016 0.002 TYR A 336 PHE 0.031 0.002 PHE B 88 TRP 0.031 0.002 TRP H 36 HIS 0.009 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (10909) covalent geometry : angle 0.63817 / 0.33 (14856) SS BOND : bond 0.00255 / 0.18 ( 16) SS BOND : angle 1.87191 / 1.14 ( 32) hydrogen bonds : bond 0.04336 / 3.11 ( 483) hydrogen bonds : angle 5.57684 / 3.94 ( 1263) link_ALPHA1-2 : bond 0.00424 / 0.22 ( 1) link_ALPHA1-2 : angle 1.86486 / 1.02 ( 3) link_ALPHA1-3 : bond 0.00011 / 0.01 ( 1) link_ALPHA1-3 : angle 1.92496 / 0.91 ( 3) link_ALPHA1-6 : bond 0.00824 / 0.43 ( 1) link_ALPHA1-6 : angle 1.19407 / 0.63 ( 3) link_BETA1-4 : bond 0.01905 / 0.91 ( 2) link_BETA1-4 : angle 3.26255 / 1.47 ( 6) link_NAG-ASN : bond 0.00605 / 0.30 ( 9) link_NAG-ASN : angle 3.24200 / 2.09 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.7814 (tpt) cc_final: 0.7483 (tpt) REVERT: A 126 LEU cc_start: 0.9592 (tp) cc_final: 0.9351 (tp) REVERT: A 137 MET cc_start: 0.8328 (tmm) cc_final: 0.7908 (tmm) REVERT: A 138 LEU cc_start: 0.9002 (mt) cc_final: 0.8600 (mt) REVERT: A 160 LEU cc_start: 0.8770 (pt) cc_final: 0.8325 (tp) REVERT: A 163 ASN cc_start: 0.8217 (m110) cc_final: 0.7861 (m-40) REVERT: A 317 TRP cc_start: 0.9173 (t60) cc_final: 0.8698 (t60) REVERT: A 318 LEU cc_start: 0.9740 (mt) cc_final: 0.9420 (mt) REVERT: A 349 GLU cc_start: 0.9325 (tt0) cc_final: 0.8947 (tt0) REVERT: A 356 MET cc_start: 0.8656 (tpp) cc_final: 0.8366 (tpp) REVERT: A 458 GLU cc_start: 0.8780 (tt0) cc_final: 0.8068 (tt0) REVERT: A 481 SER cc_start: 0.8998 (p) cc_final: 0.8798 (m) REVERT: A 579 LEU cc_start: 0.9212 (tp) cc_final: 0.8238 (pp) REVERT: A 640 GLN cc_start: 0.8911 (tt0) cc_final: 0.8165 (mt0) REVERT: B 47 ASP cc_start: 0.9108 (m-30) cc_final: 0.8753 (m-30) REVERT: B 89 PHE cc_start: 0.9085 (m-80) cc_final: 0.8521 (m-80) REVERT: B 106 GLU cc_start: 0.9310 (tt0) cc_final: 0.8758 (pt0) REVERT: C 73 ASP cc_start: 0.8342 (t0) cc_final: 0.8034 (t0) REVERT: C 81 TRP cc_start: 0.8693 (m-90) cc_final: 0.8084 (m100) REVERT: C 92 GLN cc_start: 0.9153 (mm110) cc_final: 0.8891 (mm110) REVERT: C 105 ARG cc_start: 0.9139 (tpp80) cc_final: 0.8895 (tpp80) REVERT: C 106 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8240 (mt-10) REVERT: C 125 TRP cc_start: 0.8082 (t60) cc_final: 0.7465 (t60) REVERT: C 171 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7068 (tm-30) REVERT: H 46 GLU cc_start: 0.8494 (tt0) cc_final: 0.8091 (tp30) REVERT: H 48 MET cc_start: 0.9398 (mtm) cc_final: 0.8451 (mtp) REVERT: H 69 MET cc_start: 0.7323 (mmp) cc_final: 0.6689 (mmm) REVERT: H 104 PHE cc_start: 0.8832 (m-10) cc_final: 0.8527 (m-10) REVERT: H 212 LYS cc_start: 0.9268 (tttm) cc_final: 0.8568 (mmtt) REVERT: H 215 LYS cc_start: 0.8034 (tppt) cc_final: 0.7643 (ttpt) REVERT: L 3 GLU cc_start: 0.8740 (tt0) cc_final: 0.8321 (tm-30) REVERT: L 4 LEU cc_start: 0.8742 (mt) cc_final: 0.8189 (tt) REVERT: L 86 TYR cc_start: 0.8291 (m-80) cc_final: 0.7882 (m-80) REVERT: L 136 LEU cc_start: 0.8836 (mt) cc_final: 0.8553 (mm) REVERT: L 140 ILE cc_start: 0.9428 (mp) cc_final: 0.9089 (mp) REVERT: L 143 PHE cc_start: 0.9026 (p90) cc_final: 0.8233 (p90) REVERT: L 197 CYS cc_start: 0.6561 (t) cc_final: 0.6241 (p) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.0796 time to fit residues: 25.6009 Evaluate side-chains 168 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 63 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 HIS A 657 HIS ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.066904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.051494 restraints weight = 48533.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.053389 restraints weight = 27985.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.054694 restraints weight = 18671.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.055540 restraints weight = 13843.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.056190 restraints weight = 11225.422| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10939 Z= 0.179 Angle : 0.674 10.137 14930 Z= 0.345 Chirality : 0.044 0.409 1735 Planarity : 0.005 0.046 1862 Dihedral : 4.846 23.386 1459 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.23), residues: 1336 helix: 0.68 (0.27), residues: 335 sheet: 0.62 (0.28), residues: 310 loop : -0.16 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 216 TYR 0.023 0.002 TYR H 108 PHE 0.036 0.002 PHE A 232 TRP 0.028 0.002 TRP H 36 HIS 0.010 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (10909) covalent geometry : angle 0.65359 / 0.34 (14856) SS BOND : bond 0.00362 / 0.22 ( 16) SS BOND : angle 1.25429 / 0.69 ( 32) hydrogen bonds : bond 0.04477 / 3.23 ( 483) hydrogen bonds : angle 5.63888 / 3.96 ( 1263) link_ALPHA1-2 : bond 0.00401 / 0.21 ( 1) link_ALPHA1-2 : angle 1.93343 / 1.07 ( 3) link_ALPHA1-3 : bond 0.00158 / 0.08 ( 1) link_ALPHA1-3 : angle 2.11251 / 0.99 ( 3) link_ALPHA1-6 : bond 0.00816 / 0.43 ( 1) link_ALPHA1-6 : angle 1.19634 / 0.64 ( 3) link_BETA1-4 : bond 0.01813 / 0.86 ( 2) link_BETA1-4 : angle 3.26554 / 1.47 ( 6) link_NAG-ASN : bond 0.00603 / 0.30 ( 9) link_NAG-ASN : angle 3.26342 / 2.12 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1724.14 seconds wall clock time: 30 minutes 43.98 seconds (1843.98 seconds total)