Starting phenix.real_space_refine on Tue Nov 18 04:27:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c5v_7344/11_2025/6c5v_7344.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c5v_7344/11_2025/6c5v_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_7344/11_2025/6c5v_7344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c5v_7344/11_2025/6c5v_7344.map" model { file = "/net/cci-nas-00/data/ceres_data/6c5v_7344/11_2025/6c5v_7344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c5v_7344/11_2025/6c5v_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-2.0-5881/lib/python3.9/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 dihedrals: 18 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.51, per 1000 atoms: 0.24 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: 1.20 Conformation dependent library (CDL) restraints added in 735.1 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: 0.40 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: 2.02 Time building geometry restraints manager: 1.58 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 - 21.48: 6461 21.48 - 42.95: 138 42.95 - 64.43: 53 64.43 - 85.91: 13 85.91 - 107.38: 5 Dihedral angle restraints: 6670 sinusoidal: 2751 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=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.67 107.38 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 6667 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.590 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 11.190 107.382 4114 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 covalent geometry : bond 0.01346 (10909) covalent geometry : angle 1.30377 (14856) SS BOND : bond 0.02407 ( 16) SS BOND : angle 3.87487 ( 32) hydrogen bonds : bond 0.17846 ( 483) hydrogen bonds : angle 7.70787 ( 1263) link_ALPHA1-2 : bond 0.02988 ( 1) link_ALPHA1-2 : angle 1.79106 ( 3) link_ALPHA1-3 : bond 0.04766 ( 1) link_ALPHA1-3 : angle 1.58088 ( 3) link_ALPHA1-6 : bond 0.01580 ( 1) link_ALPHA1-6 : angle 2.19658 ( 3) link_BETA1-4 : bond 0.04139 ( 2) link_BETA1-4 : angle 2.48549 ( 6) link_NAG-ASN : bond 0.02766 ( 9) link_NAG-ASN : angle 1.96292 ( 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 : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8735 (tt) cc_final: 0.8475 (mp) REVERT: A 73 LYS cc_start: 0.9077 (pttt) cc_final: 0.8847 (ttpt) REVERT: A 137 MET cc_start: 0.8720 (tpt) cc_final: 0.8475 (tmm) REVERT: A 217 THR cc_start: 0.9416 (m) cc_final: 0.9056 (t) REVERT: A 283 LEU cc_start: 0.9224 (mt) cc_final: 0.8972 (mt) REVERT: A 286 GLU cc_start: 0.8477 (tt0) cc_final: 0.8250 (tm-30) REVERT: A 317 TRP cc_start: 0.9231 (t60) cc_final: 0.8610 (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: 0.8320 (Cg_exo) REVERT: A 413 LEU cc_start: 0.9196 (mt) cc_final: 0.8799 (tp) REVERT: A 417 MET cc_start: 0.8654 (mtt) cc_final: 0.8034 (mmm) REVERT: A 466 LEU cc_start: 0.8762 (mt) cc_final: 0.8532 (tt) REVERT: A 517 LEU cc_start: 0.9530 (mt) cc_final: 0.9302 (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: 0.8893 (p) REVERT: A 582 VAL cc_start: 0.9275 (t) cc_final: 0.8976 (t) REVERT: A 614 PHE cc_start: 0.8703 (m-80) cc_final: 0.8138 (m-80) REVERT: A 661 LEU cc_start: 0.8549 (mt) cc_final: 0.8333 (mt) REVERT: B 89 PHE cc_start: 0.9082 (m-80) cc_final: 0.8539 (m-80) REVERT: B 106 GLU cc_start: 0.9335 (tt0) cc_final: 0.8833 (tm-30) REVERT: B 115 TYR cc_start: 0.7975 (t80) cc_final: 0.7464 (t80) REVERT: B 128 LEU cc_start: 0.8441 (mt) cc_final: 0.8108 (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: -0.0589 (t0) REVERT: C 116 PHE cc_start: 0.8122 (m-80) cc_final: 0.7489 (m-80) REVERT: C 155 ASN cc_start: 0.7223 (m-40) cc_final: 0.7001 (m-40) REVERT: C 169 VAL cc_start: 0.7855 (t) cc_final: 0.7644 (p) REVERT: C 171 GLU cc_start: 0.8326 (mm-30) cc_final: 0.6781 (tm-30) REVERT: C 188 PHE cc_start: 0.8755 (m-80) cc_final: 0.8518 (m-80) REVERT: C 211 LEU cc_start: 0.9069 (mt) cc_final: 0.8591 (mm) REVERT: H 25 SER cc_start: 0.7949 (t) cc_final: 0.7662 (m) REVERT: H 32 PHE cc_start: 0.8798 (m-80) cc_final: 0.8314 (m-80) REVERT: H 69 MET cc_start: 0.7626 (mtm) cc_final: 0.6911 (mtm) REVERT: H 98 MET cc_start: 0.8100 (ttt) cc_final: 0.5718 (tpt) REVERT: H 160 TRP cc_start: 0.8302 (m100) cc_final: 0.7962 (m100) REVERT: H 165 LEU cc_start: 0.8342 (tp) cc_final: 0.7842 (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: 0.8273 (tm-30) REVERT: L 4 LEU cc_start: 0.8856 (mt) cc_final: 0.8635 (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: 0.7958 (m-80) REVERT: L 75 SER cc_start: 0.8572 (t) cc_final: 0.7776 (m) REVERT: L 84 ASP cc_start: 0.8821 (m-30) cc_final: 0.8548 (m-30) REVERT: L 99 TYR cc_start: 0.7893 (m-80) cc_final: 0.7305 (m-80) REVERT: L 121 LEU cc_start: 0.8511 (tp) cc_final: 0.8204 (tt) REVERT: L 136 LEU cc_start: 0.8919 (mt) cc_final: 0.8566 (mm) REVERT: L 138 CYS cc_start: 0.7638 (t) cc_final: 0.6885 (t) REVERT: L 143 PHE cc_start: 0.8874 (p90) cc_final: 0.8355 (p90) REVERT: L 174 ASN cc_start: 0.8797 (t0) cc_final: 0.8479 (t0) outliers start: 5 outliers final: 1 residues processed: 398 average time/residue: 0.1041 time to fit residues: 58.0397 Evaluate side-chains 232 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 230 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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: 1.9990 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS B 103 HIS H 61 GLN L 88 GLN L 96 HIS L 192 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.069802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.054662 restraints weight = 45509.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.056736 restraints weight = 25823.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.058149 restraints weight = 17059.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.059102 restraints weight = 12574.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.059791 restraints weight = 10099.398| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10939 Z= 0.197 Angle : 0.723 11.797 14930 Z= 0.373 Chirality : 0.045 0.272 1735 Planarity : 0.005 0.041 1862 Dihedral : 8.213 83.215 1745 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: 0.54 (0.22), residues: 1336 helix: 0.65 (0.26), residues: 337 sheet: 0.88 (0.28), residues: 315 loop : 0.08 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 418 TYR 0.025 0.002 TYR C 185 PHE 0.024 0.003 PHE L 101 TRP 0.014 0.002 TRP H 36 HIS 0.008 0.002 HIS H 206 Details of bonding type rmsd covalent geometry : bond 0.00423 (10909) covalent geometry : angle 0.69991 (14856) SS BOND : bond 0.00371 ( 16) SS BOND : angle 1.18215 ( 32) hydrogen bonds : bond 0.05767 ( 483) hydrogen bonds : angle 5.95063 ( 1263) link_ALPHA1-2 : bond 0.00297 ( 1) link_ALPHA1-2 : angle 1.47843 ( 3) link_ALPHA1-3 : bond 0.00566 ( 1) link_ALPHA1-3 : angle 2.13316 ( 3) link_ALPHA1-6 : bond 0.01187 ( 1) link_ALPHA1-6 : angle 1.42870 ( 3) link_BETA1-4 : bond 0.02105 ( 2) link_BETA1-4 : angle 3.50067 ( 6) link_NAG-ASN : bond 0.01043 ( 9) link_NAG-ASN : angle 3.74102 ( 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 286 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8472 (tt) cc_final: 0.8115 (mp) REVERT: A 137 MET cc_start: 0.8363 (tpt) cc_final: 0.8042 (tpp) REVERT: A 138 LEU cc_start: 0.9319 (mt) cc_final: 0.8742 (mt) REVERT: A 217 THR cc_start: 0.9389 (m) cc_final: 0.9115 (t) REVERT: A 317 TRP cc_start: 0.9062 (t60) cc_final: 0.8463 (t60) REVERT: A 318 LEU cc_start: 0.9637 (mt) cc_final: 0.9327 (mt) REVERT: A 349 GLU cc_start: 0.9284 (tt0) cc_final: 0.8955 (tt0) REVERT: A 413 LEU cc_start: 0.8870 (mt) cc_final: 0.8467 (tp) REVERT: A 417 MET cc_start: 0.8420 (mtt) cc_final: 0.8086 (mmm) REVERT: A 458 GLU cc_start: 0.8406 (tt0) cc_final: 0.7466 (tt0) REVERT: A 494 MET cc_start: 0.8216 (ttm) cc_final: 0.7918 (ttm) REVERT: A 537 ARG cc_start: 0.8190 (mmt-90) cc_final: 0.7943 (mtt180) REVERT: A 551 THR cc_start: 0.9425 (m) cc_final: 0.9002 (p) REVERT: A 614 PHE cc_start: 0.8654 (m-80) cc_final: 0.8272 (m-80) REVERT: A 635 THR cc_start: 0.9286 (p) cc_final: 0.9023 (t) REVERT: A 649 PHE cc_start: 0.8329 (m-80) cc_final: 0.8036 (m-80) REVERT: B 81 ASN cc_start: 0.8960 (t0) cc_final: 0.8141 (t0) REVERT: B 88 PHE cc_start: 0.8777 (t80) cc_final: 0.8470 (t80) REVERT: B 89 PHE cc_start: 0.9111 (m-80) cc_final: 0.8495 (m-80) REVERT: B 106 GLU cc_start: 0.9285 (tt0) cc_final: 0.8726 (tm-30) REVERT: B 112 GLU cc_start: 0.9243 (pt0) cc_final: 0.8980 (pt0) REVERT: B 128 LEU cc_start: 0.8522 (mt) cc_final: 0.8139 (mm) REVERT: C 81 TRP cc_start: 0.8646 (m-90) cc_final: 0.8133 (m100) REVERT: C 116 PHE cc_start: 0.8257 (m-80) cc_final: 0.7283 (m-80) REVERT: C 171 GLU cc_start: 0.8063 (mm-30) cc_final: 0.6659 (tm-30) REVERT: C 182 PHE cc_start: 0.7778 (m-10) cc_final: 0.7575 (m-80) REVERT: C 198 PHE cc_start: 0.8886 (m-10) cc_final: 0.8573 (m-10) REVERT: C 211 LEU cc_start: 0.8713 (mt) cc_final: 0.8505 (mm) REVERT: H 32 PHE cc_start: 0.8719 (m-80) cc_final: 0.7960 (m-80) REVERT: H 52 ASP cc_start: 0.8921 (t0) cc_final: 0.8664 (t0) REVERT: H 97 GLU cc_start: 0.6898 (tm-30) cc_final: 0.6163 (tm-30) REVERT: H 98 MET cc_start: 0.6625 (ttt) cc_final: 0.5973 (tpt) REVERT: H 101 ARG cc_start: 0.8645 (ptp-170) cc_final: 0.8290 (ptp-170) REVERT: L 3 GLU cc_start: 0.8562 (tt0) cc_final: 0.8274 (tm-30) REVERT: L 4 LEU cc_start: 0.8793 (mt) cc_final: 0.8529 (tp) REVERT: L 20 ILE cc_start: 0.9358 (mm) cc_final: 0.9082 (pt) REVERT: L 84 ASP cc_start: 0.8882 (m-30) cc_final: 0.8592 (m-30) REVERT: L 99 TYR cc_start: 0.8098 (m-80) cc_final: 0.6064 (m-10) REVERT: L 109 VAL cc_start: 0.8040 (t) cc_final: 0.7787 (t) REVERT: L 128 GLU cc_start: 0.9265 (tp30) cc_final: 0.8826 (tp30) REVERT: L 136 LEU cc_start: 0.8856 (mt) cc_final: 0.8522 (mm) REVERT: L 143 PHE cc_start: 0.8929 (p90) cc_final: 0.8306 (p90) REVERT: L 174 ASN cc_start: 0.8620 (t0) cc_final: 0.8247 (t0) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.0981 time to fit residues: 40.2940 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 : 0.467 ------------------------------------------------------------------------------- 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: 0.8980 chunk 127 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN 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 = 0.3205 r_free = 0.3205 target = 0.069718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.054410 restraints weight = 47077.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.056446 restraints weight = 26398.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.057820 restraints weight = 17374.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.058721 restraints weight = 12818.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.059408 restraints weight = 10329.309| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10939 Z= 0.140 Angle : 0.631 10.717 14930 Z= 0.326 Chirality : 0.044 0.277 1735 Planarity : 0.005 0.052 1862 Dihedral : 7.517 76.913 1745 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.09 % Allowed : 2.50 % Favored : 97.42 % 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: 0.48 (0.23), residues: 1336 helix: 0.60 (0.26), residues: 350 sheet: 0.78 (0.29), residues: 315 loop : 0.06 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 17 TYR 0.022 0.002 TYR C 185 PHE 0.027 0.002 PHE C 88 TRP 0.016 0.002 TRP L 189 HIS 0.006 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00296 (10909) covalent geometry : angle 0.61004 (14856) SS BOND : bond 0.00303 ( 16) SS BOND : angle 1.07942 ( 32) hydrogen bonds : bond 0.04964 ( 483) hydrogen bonds : angle 5.47294 ( 1263) link_ALPHA1-2 : bond 0.00385 ( 1) link_ALPHA1-2 : angle 1.64855 ( 3) link_ALPHA1-3 : bond 0.00492 ( 1) link_ALPHA1-3 : angle 1.86004 ( 3) link_ALPHA1-6 : bond 0.01077 ( 1) link_ALPHA1-6 : angle 1.36535 ( 3) link_BETA1-4 : bond 0.02167 ( 2) link_BETA1-4 : angle 3.41871 ( 6) link_NAG-ASN : bond 0.00614 ( 9) link_NAG-ASN : angle 3.21832 ( 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 262 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9005 (mtt) cc_final: 0.8226 (mmm) REVERT: A 137 MET cc_start: 0.8356 (tpt) cc_final: 0.8110 (tpp) REVERT: A 138 LEU cc_start: 0.9338 (mt) cc_final: 0.8788 (mt) REVERT: A 160 LEU cc_start: 0.8431 (pt) cc_final: 0.7980 (tp) REVERT: A 217 THR cc_start: 0.9323 (m) cc_final: 0.9042 (t) REVERT: A 256 MET cc_start: 0.9067 (tpp) cc_final: 0.8405 (tpp) REVERT: A 317 TRP cc_start: 0.8995 (t60) cc_final: 0.8396 (t60) REVERT: A 318 LEU cc_start: 0.9700 (mt) cc_final: 0.9271 (mt) REVERT: A 349 GLU cc_start: 0.9169 (tt0) cc_final: 0.8836 (tt0) REVERT: A 413 LEU cc_start: 0.8763 (mt) cc_final: 0.8414 (tp) REVERT: A 417 MET cc_start: 0.8551 (mtt) cc_final: 0.8175 (mmm) REVERT: A 458 GLU cc_start: 0.8705 (tt0) cc_final: 0.7824 (tt0) REVERT: A 537 ARG cc_start: 0.8262 (mmt-90) cc_final: 0.7975 (mtt180) REVERT: A 551 THR cc_start: 0.9393 (m) cc_final: 0.8948 (p) REVERT: A 582 VAL cc_start: 0.9129 (t) cc_final: 0.8886 (t) REVERT: A 614 PHE cc_start: 0.8773 (m-80) cc_final: 0.8338 (m-10) REVERT: A 649 PHE cc_start: 0.8444 (m-80) cc_final: 0.8173 (m-80) REVERT: B 81 ASN cc_start: 0.8859 (t0) cc_final: 0.8135 (t0) REVERT: B 84 ASN cc_start: 0.9109 (m-40) cc_final: 0.8904 (m-40) REVERT: B 89 PHE cc_start: 0.9155 (m-80) cc_final: 0.8153 (m-80) REVERT: B 106 GLU cc_start: 0.9364 (tt0) cc_final: 0.8759 (tm-30) REVERT: B 112 GLU cc_start: 0.9218 (pt0) cc_final: 0.8965 (pt0) REVERT: B 128 LEU cc_start: 0.8449 (mt) cc_final: 0.8219 (mm) REVERT: C 81 TRP cc_start: 0.8666 (m-90) cc_final: 0.8129 (m100) REVERT: C 92 GLN cc_start: 0.8937 (mm110) cc_final: 0.8672 (mm110) REVERT: C 116 PHE cc_start: 0.8101 (m-80) cc_final: 0.7274 (m-80) REVERT: C 198 PHE cc_start: 0.8911 (m-10) cc_final: 0.8660 (m-10) REVERT: C 211 LEU cc_start: 0.8784 (mt) cc_final: 0.8545 (mm) REVERT: H 25 SER cc_start: 0.8053 (t) cc_final: 0.7848 (m) REVERT: H 48 MET cc_start: 0.9378 (mtm) cc_final: 0.8255 (mpp) REVERT: H 98 MET cc_start: 0.6772 (ttt) cc_final: 0.6032 (tpt) REVERT: H 101 ARG cc_start: 0.8826 (ptp-170) cc_final: 0.8406 (ptp-170) REVERT: H 212 LYS cc_start: 0.9030 (tttp) cc_final: 0.7966 (mmtt) REVERT: L 3 GLU cc_start: 0.8644 (tt0) cc_final: 0.8265 (tm-30) REVERT: L 4 LEU cc_start: 0.8760 (mt) cc_final: 0.8494 (tp) REVERT: L 20 ILE cc_start: 0.9379 (mm) cc_final: 0.9135 (pt) REVERT: L 46 VAL cc_start: 0.9448 (m) cc_final: 0.9222 (p) REVERT: L 84 ASP cc_start: 0.8815 (m-30) cc_final: 0.8578 (m-30) REVERT: L 99 TYR cc_start: 0.8188 (m-80) cc_final: 0.5829 (m-10) REVERT: L 128 GLU cc_start: 0.9149 (tp30) cc_final: 0.8711 (tp30) REVERT: L 136 LEU cc_start: 0.8811 (mt) cc_final: 0.8406 (mm) REVERT: L 143 PHE cc_start: 0.8979 (p90) cc_final: 0.8154 (p90) REVERT: L 174 ASN cc_start: 0.8640 (t0) cc_final: 0.8282 (t0) REVERT: L 184 LEU cc_start: 0.7894 (mt) cc_final: 0.7520 (tp) outliers start: 1 outliers final: 0 residues processed: 261 average time/residue: 0.0899 time to fit residues: 34.7685 Evaluate side-chains 207 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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: 1.9990 chunk 44 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS A 426 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 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 = 0.3161 r_free = 0.3161 target = 0.067828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.052465 restraints weight = 48506.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.054434 restraints weight = 27454.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.055783 restraints weight = 18242.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.056689 restraints weight = 13536.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.057285 restraints weight = 10935.273| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4102 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= 0.191 Angle : 0.666 10.507 14930 Z= 0.340 Chirality : 0.043 0.251 1735 Planarity : 0.005 0.042 1862 Dihedral : 7.281 70.098 1745 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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 (0.22), residues: 1336 helix: 0.79 (0.27), residues: 339 sheet: 0.62 (0.28), residues: 321 loop : -0.01 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 524 TYR 0.017 0.002 TYR C 136 PHE 0.020 0.002 PHE A 298 TRP 0.022 0.002 TRP H 160 HIS 0.008 0.002 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00404 (10909) covalent geometry : angle 0.64387 (14856) SS BOND : bond 0.00420 ( 16) SS BOND : angle 1.00372 ( 32) hydrogen bonds : bond 0.04814 ( 483) hydrogen bonds : angle 5.58873 ( 1263) link_ALPHA1-2 : bond 0.00230 ( 1) link_ALPHA1-2 : angle 1.73591 ( 3) link_ALPHA1-3 : bond 0.00266 ( 1) link_ALPHA1-3 : angle 2.15844 ( 3) link_ALPHA1-6 : bond 0.01147 ( 1) link_ALPHA1-6 : angle 1.10679 ( 3) link_BETA1-4 : bond 0.02343 ( 2) link_BETA1-4 : angle 3.65863 ( 6) link_NAG-ASN : bond 0.00637 ( 9) link_NAG-ASN : angle 3.42143 ( 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 : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8581 (mtt) cc_final: 0.8329 (mmm) REVERT: A 160 LEU cc_start: 0.8636 (pt) cc_final: 0.8211 (tp) REVERT: A 217 THR cc_start: 0.9351 (m) cc_final: 0.9110 (t) REVERT: A 283 LEU cc_start: 0.8924 (mt) cc_final: 0.8715 (mt) REVERT: A 317 TRP cc_start: 0.9122 (t60) cc_final: 0.8589 (t60) REVERT: A 318 LEU cc_start: 0.9626 (mt) cc_final: 0.9332 (mt) REVERT: A 349 GLU cc_start: 0.9230 (tt0) cc_final: 0.8874 (tt0) REVERT: A 378 LEU cc_start: 0.9612 (pp) cc_final: 0.9218 (mt) REVERT: A 413 LEU cc_start: 0.8734 (mt) cc_final: 0.8385 (tp) REVERT: A 417 MET cc_start: 0.8726 (mtt) cc_final: 0.8405 (mmm) REVERT: A 458 GLU cc_start: 0.8719 (tt0) cc_final: 0.7813 (tt0) REVERT: A 614 PHE cc_start: 0.8766 (m-80) cc_final: 0.8270 (m-80) REVERT: A 649 PHE cc_start: 0.8424 (m-80) cc_final: 0.8118 (m-80) REVERT: B 81 ASN cc_start: 0.8840 (t0) cc_final: 0.8153 (t0) REVERT: B 84 ASN cc_start: 0.9124 (m-40) cc_final: 0.8911 (m-40) REVERT: B 89 PHE cc_start: 0.9022 (m-80) cc_final: 0.8214 (m-80) REVERT: B 106 GLU cc_start: 0.9367 (tt0) cc_final: 0.8775 (tm-30) REVERT: B 107 LEU cc_start: 0.9576 (tp) cc_final: 0.9367 (tp) REVERT: B 112 GLU cc_start: 0.9271 (pt0) cc_final: 0.8949 (pt0) REVERT: B 128 LEU cc_start: 0.8557 (mt) cc_final: 0.8311 (mm) REVERT: C 73 ASP cc_start: 0.7041 (t0) cc_final: 0.6654 (t0) REVERT: C 81 TRP cc_start: 0.8894 (m-90) cc_final: 0.8044 (m100) REVERT: C 92 GLN cc_start: 0.8960 (mm110) cc_final: 0.8658 (mm110) REVERT: C 105 ARG cc_start: 0.9333 (tpp80) cc_final: 0.9039 (tpp80) REVERT: C 116 PHE cc_start: 0.8235 (m-80) cc_final: 0.7563 (m-80) REVERT: C 198 PHE cc_start: 0.8997 (m-10) cc_final: 0.8747 (m-10) REVERT: C 211 LEU cc_start: 0.8972 (mt) cc_final: 0.8682 (mm) REVERT: H 20 VAL cc_start: 0.9545 (t) cc_final: 0.8283 (t) REVERT: H 25 SER cc_start: 0.8107 (t) cc_final: 0.7846 (m) REVERT: H 48 MET cc_start: 0.9314 (mtm) cc_final: 0.8294 (mtp) REVERT: H 80 MET cc_start: 0.8951 (ttp) cc_final: 0.8722 (ppp) REVERT: H 97 GLU cc_start: 0.6692 (tm-30) cc_final: 0.6180 (tm-30) REVERT: H 98 MET cc_start: 0.6828 (ttt) cc_final: 0.6177 (tpt) REVERT: H 212 LYS cc_start: 0.9078 (tttp) cc_final: 0.8032 (mmtt) REVERT: L 3 GLU cc_start: 0.8649 (tt0) cc_final: 0.8293 (tm-30) REVERT: L 4 LEU cc_start: 0.8742 (mt) cc_final: 0.8420 (tt) REVERT: L 99 TYR cc_start: 0.8359 (m-80) cc_final: 0.5949 (m-10) REVERT: L 128 GLU cc_start: 0.9170 (tp30) cc_final: 0.8691 (tp30) REVERT: L 136 LEU cc_start: 0.8782 (mt) cc_final: 0.8400 (mm) REVERT: L 143 PHE cc_start: 0.9062 (p90) cc_final: 0.8243 (p90) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.0843 time to fit residues: 31.3403 Evaluate side-chains 184 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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: 4.9990 chunk 75 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS A 657 HIS H 170 HIS ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.064613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.049408 restraints weight = 48804.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.051222 restraints weight = 28397.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.052440 restraints weight = 19069.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.053242 restraints weight = 14260.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.053852 restraints weight = 11645.754| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10939 Z= 0.296 Angle : 0.807 9.975 14930 Z= 0.414 Chirality : 0.046 0.214 1735 Planarity : 0.006 0.045 1862 Dihedral : 7.391 62.206 1745 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % 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: -0.10 (0.22), residues: 1336 helix: 0.29 (0.26), residues: 339 sheet: 0.36 (0.27), residues: 319 loop : -0.36 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 516 TYR 0.031 0.003 TYR A 389 PHE 0.026 0.003 PHE B 89 TRP 0.023 0.003 TRP H 160 HIS 0.009 0.002 HIS A 528 Details of bonding type rmsd covalent geometry : bond 0.00620 (10909) covalent geometry : angle 0.78220 (14856) SS BOND : bond 0.00497 ( 16) SS BOND : angle 2.14313 ( 32) hydrogen bonds : bond 0.05316 ( 483) hydrogen bonds : angle 6.08355 ( 1263) link_ALPHA1-2 : bond 0.00306 ( 1) link_ALPHA1-2 : angle 2.42842 ( 3) link_ALPHA1-3 : bond 0.00094 ( 1) link_ALPHA1-3 : angle 2.39523 ( 3) link_ALPHA1-6 : bond 0.01490 ( 1) link_ALPHA1-6 : angle 1.02920 ( 3) link_BETA1-4 : bond 0.02545 ( 2) link_BETA1-4 : angle 4.01607 ( 6) link_NAG-ASN : bond 0.00858 ( 9) link_NAG-ASN : angle 3.60097 ( 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 214 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.9158 (mp0) cc_final: 0.8905 (mp0) REVERT: A 91 ASP cc_start: 0.8305 (p0) cc_final: 0.8003 (p0) REVERT: A 121 MET cc_start: 0.8783 (mtt) cc_final: 0.8525 (mmm) REVERT: A 138 LEU cc_start: 0.9349 (mt) cc_final: 0.8836 (mt) REVERT: A 160 LEU cc_start: 0.8790 (pt) cc_final: 0.8228 (tp) REVERT: A 217 THR cc_start: 0.9239 (m) cc_final: 0.9026 (t) REVERT: A 318 LEU cc_start: 0.9705 (mt) cc_final: 0.9466 (mt) REVERT: A 349 GLU cc_start: 0.9350 (tt0) cc_final: 0.8930 (tt0) REVERT: A 458 GLU cc_start: 0.8612 (tt0) cc_final: 0.7714 (tt0) REVERT: A 579 LEU cc_start: 0.9429 (tp) cc_final: 0.8406 (pp) REVERT: B 81 ASN cc_start: 0.8666 (t0) cc_final: 0.8326 (t0) REVERT: B 89 PHE cc_start: 0.9148 (m-80) cc_final: 0.8540 (m-80) REVERT: B 106 GLU cc_start: 0.9347 (tt0) cc_final: 0.8697 (tm-30) REVERT: B 107 LEU cc_start: 0.9553 (tp) cc_final: 0.9319 (tp) REVERT: B 112 GLU cc_start: 0.9283 (pt0) cc_final: 0.9064 (pt0) REVERT: C 105 ARG cc_start: 0.9375 (tpp80) cc_final: 0.9047 (tpp80) REVERT: C 116 PHE cc_start: 0.8383 (m-80) cc_final: 0.7140 (m-80) REVERT: C 125 TRP cc_start: 0.8151 (t60) cc_final: 0.7493 (t60) REVERT: C 171 GLU cc_start: 0.8029 (mm-30) cc_final: 0.6961 (tm-30) REVERT: C 198 PHE cc_start: 0.8902 (m-10) cc_final: 0.8699 (m-10) REVERT: H 25 SER cc_start: 0.8145 (t) cc_final: 0.7724 (m) REVERT: H 46 GLU cc_start: 0.8521 (tt0) cc_final: 0.8010 (tp30) REVERT: H 48 MET cc_start: 0.9356 (mtm) cc_final: 0.8481 (mtp) REVERT: H 80 MET cc_start: 0.9341 (ttp) cc_final: 0.8546 (tmm) REVERT: H 98 MET cc_start: 0.7413 (ttt) cc_final: 0.6949 (tpt) REVERT: H 104 PHE cc_start: 0.9166 (m-80) cc_final: 0.7996 (m-80) REVERT: H 212 LYS cc_start: 0.9225 (tttp) cc_final: 0.8486 (mptt) REVERT: H 215 LYS cc_start: 0.8607 (tppt) cc_final: 0.8393 (ttpt) REVERT: L 3 GLU cc_start: 0.8742 (tt0) cc_final: 0.8322 (tm-30) REVERT: L 4 LEU cc_start: 0.8828 (mt) cc_final: 0.8411 (mm) REVERT: L 81 ASP cc_start: 0.8188 (m-30) cc_final: 0.7555 (m-30) REVERT: L 99 TYR cc_start: 0.8695 (m-80) cc_final: 0.5900 (m-80) REVERT: L 136 LEU cc_start: 0.8601 (mt) cc_final: 0.8253 (mm) REVERT: L 140 ILE cc_start: 0.9459 (mp) cc_final: 0.9155 (mp) REVERT: L 143 PHE cc_start: 0.8980 (p90) cc_final: 0.8162 (p90) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.0812 time to fit residues: 26.5009 Evaluate side-chains 164 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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: 0.9990 chunk 123 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN H 170 HIS L 25 HIS ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS L 198 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.067662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.052543 restraints weight = 48215.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.054516 restraints weight = 27325.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.055861 restraints weight = 17990.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.056787 restraints weight = 13200.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.057387 restraints weight = 10548.653| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 10939 Z= 0.134 Angle : 0.656 12.624 14930 Z= 0.329 Chirality : 0.045 0.248 1735 Planarity : 0.005 0.059 1862 Dihedral : 6.600 59.733 1745 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % 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: 0.37 (0.23), residues: 1336 helix: 0.73 (0.27), residues: 341 sheet: 0.70 (0.27), residues: 315 loop : -0.13 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 71 TYR 0.013 0.002 TYR C 117 PHE 0.024 0.002 PHE A 232 TRP 0.011 0.001 TRP L 189 HIS 0.008 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00288 (10909) covalent geometry : angle 0.63564 (14856) SS BOND : bond 0.00325 ( 16) SS BOND : angle 1.27143 ( 32) hydrogen bonds : bond 0.04506 ( 483) hydrogen bonds : angle 5.51034 ( 1263) link_ALPHA1-2 : bond 0.00568 ( 1) link_ALPHA1-2 : angle 1.77884 ( 3) link_ALPHA1-3 : bond 0.00552 ( 1) link_ALPHA1-3 : angle 2.19182 ( 3) link_ALPHA1-6 : bond 0.01025 ( 1) link_ALPHA1-6 : angle 1.24201 ( 3) link_BETA1-4 : bond 0.02164 ( 2) link_BETA1-4 : angle 3.49086 ( 6) link_NAG-ASN : bond 0.00585 ( 9) link_NAG-ASN : angle 3.11340 ( 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 240 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASP cc_start: 0.8274 (p0) cc_final: 0.8037 (p0) REVERT: A 103 ASP cc_start: 0.8528 (t0) cc_final: 0.8292 (t70) REVERT: A 121 MET cc_start: 0.8716 (mtt) cc_final: 0.8388 (mmm) REVERT: A 138 LEU cc_start: 0.9361 (mt) cc_final: 0.8988 (mt) REVERT: A 160 LEU cc_start: 0.8584 (pt) cc_final: 0.8255 (tp) REVERT: A 163 ASN cc_start: 0.8324 (m-40) cc_final: 0.7979 (m-40) REVERT: A 217 THR cc_start: 0.9224 (m) cc_final: 0.8946 (t) REVERT: A 317 TRP cc_start: 0.9171 (t60) cc_final: 0.8695 (t60) REVERT: A 318 LEU cc_start: 0.9644 (mt) cc_final: 0.9430 (pp) REVERT: A 349 GLU cc_start: 0.9241 (tt0) cc_final: 0.8891 (tt0) REVERT: A 417 MET cc_start: 0.8911 (mpp) cc_final: 0.8228 (ptp) REVERT: A 458 GLU cc_start: 0.8865 (tt0) cc_final: 0.8192 (tt0) REVERT: A 640 GLN cc_start: 0.9052 (tt0) cc_final: 0.8844 (tt0) REVERT: B 81 ASN cc_start: 0.8593 (t0) cc_final: 0.8345 (t0) REVERT: B 88 PHE cc_start: 0.8858 (t80) cc_final: 0.7740 (t80) REVERT: B 89 PHE cc_start: 0.8957 (m-80) cc_final: 0.8338 (m-80) REVERT: B 100 LEU cc_start: 0.9104 (mt) cc_final: 0.8683 (mt) REVERT: C 81 TRP cc_start: 0.8840 (m-90) cc_final: 0.7861 (m100) REVERT: C 105 ARG cc_start: 0.9367 (tpp80) cc_final: 0.9012 (tpp80) REVERT: C 106 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8256 (mt-10) REVERT: C 116 PHE cc_start: 0.7838 (m-80) cc_final: 0.6864 (m-80) REVERT: C 134 GLU cc_start: 0.8752 (pm20) cc_final: 0.8459 (pm20) REVERT: C 198 PHE cc_start: 0.8939 (m-10) cc_final: 0.8728 (m-10) REVERT: H 46 GLU cc_start: 0.8517 (tt0) cc_final: 0.8035 (tp30) REVERT: H 48 MET cc_start: 0.9396 (mtm) cc_final: 0.8426 (mtp) REVERT: H 80 MET cc_start: 0.9283 (ttp) cc_final: 0.8510 (tmm) REVERT: H 160 TRP cc_start: 0.8408 (m100) cc_final: 0.8156 (m100) REVERT: H 212 LYS cc_start: 0.9176 (tttp) cc_final: 0.8489 (mmtt) REVERT: H 215 LYS cc_start: 0.8519 (tppt) cc_final: 0.8025 (tptp) REVERT: L 3 GLU cc_start: 0.8767 (tt0) cc_final: 0.8240 (tm-30) REVERT: L 4 LEU cc_start: 0.8788 (mt) cc_final: 0.8302 (tp) REVERT: L 81 ASP cc_start: 0.8053 (m-30) cc_final: 0.7118 (m-30) REVERT: L 86 TYR cc_start: 0.8423 (m-80) cc_final: 0.7829 (m-10) REVERT: L 128 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8655 (tp30) REVERT: L 136 LEU cc_start: 0.8472 (mt) cc_final: 0.8259 (mm) REVERT: L 140 ILE cc_start: 0.9458 (mp) cc_final: 0.9173 (mp) REVERT: L 143 PHE cc_start: 0.9006 (p90) cc_final: 0.8166 (p90) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.0843 time to fit residues: 30.3985 Evaluate side-chains 180 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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: 7.9990 chunk 75 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.065762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.050505 restraints weight = 48857.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.052381 restraints weight = 27995.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.053638 restraints weight = 18602.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.054499 restraints weight = 13825.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.055087 restraints weight = 11198.596| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10939 Z= 0.211 Angle : 0.712 10.075 14930 Z= 0.362 Chirality : 0.044 0.228 1735 Planarity : 0.005 0.056 1862 Dihedral : 6.543 56.403 1745 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.17 % Allowed : 1.12 % 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: 0.21 (0.23), residues: 1336 helix: 0.62 (0.27), residues: 342 sheet: 0.57 (0.28), residues: 313 loop : -0.23 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 71 TYR 0.024 0.002 TYR B 115 PHE 0.028 0.002 PHE B 88 TRP 0.025 0.002 TRP L 189 HIS 0.007 0.002 HIS A 528 Details of bonding type rmsd covalent geometry : bond 0.00453 (10909) covalent geometry : angle 0.69101 (14856) SS BOND : bond 0.00396 ( 16) SS BOND : angle 1.73934 ( 32) hydrogen bonds : bond 0.04702 ( 483) hydrogen bonds : angle 5.90306 ( 1263) link_ALPHA1-2 : bond 0.00508 ( 1) link_ALPHA1-2 : angle 2.23165 ( 3) link_ALPHA1-3 : bond 0.00514 ( 1) link_ALPHA1-3 : angle 2.34133 ( 3) link_ALPHA1-6 : bond 0.01313 ( 1) link_ALPHA1-6 : angle 1.04123 ( 3) link_BETA1-4 : bond 0.02145 ( 2) link_BETA1-4 : angle 3.86526 ( 6) link_NAG-ASN : bond 0.00592 ( 9) link_NAG-ASN : angle 3.05720 ( 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 216 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 214 time to evaluate : 0.430 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 91 ASP cc_start: 0.8325 (p0) cc_final: 0.8107 (p0) REVERT: A 103 ASP cc_start: 0.8533 (t0) cc_final: 0.8314 (t70) REVERT: A 138 LEU cc_start: 0.9310 (mt) cc_final: 0.8981 (mt) REVERT: A 160 LEU cc_start: 0.8897 (pt) cc_final: 0.8419 (tp) REVERT: A 317 TRP cc_start: 0.9340 (t60) cc_final: 0.8708 (t60) REVERT: A 318 LEU cc_start: 0.9711 (mt) cc_final: 0.9401 (mt) REVERT: A 349 GLU cc_start: 0.9367 (tt0) cc_final: 0.9075 (tt0) REVERT: A 458 GLU cc_start: 0.8845 (tt0) cc_final: 0.8069 (tt0) REVERT: A 579 LEU cc_start: 0.9354 (tp) cc_final: 0.8322 (pp) REVERT: B 88 PHE cc_start: 0.9291 (t80) cc_final: 0.8866 (t80) REVERT: B 89 PHE cc_start: 0.9089 (m-80) cc_final: 0.8390 (m-80) REVERT: C 92 GLN cc_start: 0.9102 (mm110) cc_final: 0.8865 (mm110) REVERT: C 105 ARG cc_start: 0.9353 (tpp80) cc_final: 0.9062 (tpp80) REVERT: C 116 PHE cc_start: 0.8004 (m-80) cc_final: 0.6851 (m-80) REVERT: C 125 TRP cc_start: 0.7986 (t60) cc_final: 0.7201 (t60) REVERT: C 171 GLU cc_start: 0.8065 (mm-30) cc_final: 0.6943 (tm-30) REVERT: C 198 PHE cc_start: 0.8968 (m-10) cc_final: 0.8685 (m-10) REVERT: H 46 GLU cc_start: 0.8624 (tt0) cc_final: 0.8008 (tp30) REVERT: H 48 MET cc_start: 0.9428 (mtm) cc_final: 0.8381 (mtp) REVERT: H 80 MET cc_start: 0.9256 (ttp) cc_final: 0.8590 (tmm) REVERT: H 212 LYS cc_start: 0.9212 (tttm) cc_final: 0.8561 (mmtt) REVERT: H 215 LYS cc_start: 0.8282 (tppt) cc_final: 0.7886 (tptp) REVERT: L 3 GLU cc_start: 0.8794 (tt0) cc_final: 0.8334 (tm-30) REVERT: L 4 LEU cc_start: 0.8725 (mt) cc_final: 0.8192 (tt) REVERT: L 136 LEU cc_start: 0.8558 (mt) cc_final: 0.8229 (mm) REVERT: L 140 ILE cc_start: 0.9441 (mp) cc_final: 0.9112 (mp) REVERT: L 143 PHE cc_start: 0.9000 (p90) cc_final: 0.8224 (p90) REVERT: L 197 CYS cc_start: 0.6906 (t) cc_final: 0.6399 (p) outliers start: 2 outliers final: 0 residues processed: 214 average time/residue: 0.0952 time to fit residues: 30.3284 Evaluate side-chains 165 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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: 4.9990 chunk 117 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 7 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 205 ASN ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.065701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.050654 restraints weight = 48809.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.052479 restraints weight = 28048.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.053688 restraints weight = 18712.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.054574 restraints weight = 13939.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.055031 restraints weight = 11246.906| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10939 Z= 0.200 Angle : 0.698 10.043 14930 Z= 0.356 Chirality : 0.045 0.263 1735 Planarity : 0.005 0.045 1862 Dihedral : 6.472 59.992 1745 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: 0.21 (0.23), residues: 1336 helix: 0.61 (0.27), residues: 344 sheet: 0.53 (0.28), residues: 314 loop : -0.20 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 71 TYR 0.022 0.002 TYR B 115 PHE 0.022 0.002 PHE A 238 TRP 0.027 0.002 TRP H 160 HIS 0.007 0.001 HIS A 528 Details of bonding type rmsd covalent geometry : bond 0.00429 (10909) covalent geometry : angle 0.67062 (14856) SS BOND : bond 0.00509 ( 16) SS BOND : angle 1.81201 ( 32) hydrogen bonds : bond 0.04688 ( 483) hydrogen bonds : angle 5.83290 ( 1263) link_ALPHA1-2 : bond 0.00585 ( 1) link_ALPHA1-2 : angle 2.24448 ( 3) link_ALPHA1-3 : bond 0.00577 ( 1) link_ALPHA1-3 : angle 2.36172 ( 3) link_ALPHA1-6 : bond 0.01171 ( 1) link_ALPHA1-6 : angle 1.03588 ( 3) link_BETA1-4 : bond 0.02133 ( 2) link_BETA1-4 : angle 3.80642 ( 6) link_NAG-ASN : bond 0.00566 ( 9) link_NAG-ASN : angle 3.63278 ( 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 215 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASP cc_start: 0.8283 (p0) cc_final: 0.8083 (p0) REVERT: A 160 LEU cc_start: 0.8637 (pt) cc_final: 0.8364 (tp) REVERT: A 313 VAL cc_start: 0.9531 (p) cc_final: 0.9323 (m) REVERT: A 317 TRP cc_start: 0.9285 (t60) cc_final: 0.8708 (t60) REVERT: A 318 LEU cc_start: 0.9728 (mt) cc_final: 0.9469 (mt) REVERT: A 349 GLU cc_start: 0.9338 (tt0) cc_final: 0.8978 (tt0) REVERT: A 458 GLU cc_start: 0.8905 (tt0) cc_final: 0.8085 (tt0) REVERT: A 494 MET cc_start: 0.8654 (ttp) cc_final: 0.8354 (ttp) REVERT: A 579 LEU cc_start: 0.9299 (tp) cc_final: 0.8264 (pp) REVERT: B 81 ASN cc_start: 0.8441 (t0) cc_final: 0.7916 (t0) REVERT: B 88 PHE cc_start: 0.9303 (t80) cc_final: 0.9101 (t80) REVERT: B 106 GLU cc_start: 0.9327 (tt0) cc_final: 0.8742 (pt0) REVERT: C 75 GLU cc_start: 0.7323 (tp30) cc_final: 0.7108 (tp30) REVERT: C 92 GLN cc_start: 0.9096 (mm110) cc_final: 0.8860 (mm110) REVERT: C 105 ARG cc_start: 0.9352 (tpp80) cc_final: 0.9054 (tpp80) REVERT: C 116 PHE cc_start: 0.8025 (m-80) cc_final: 0.6896 (m-80) REVERT: C 125 TRP cc_start: 0.7922 (t60) cc_final: 0.7244 (t60) REVERT: C 134 GLU cc_start: 0.8630 (pm20) cc_final: 0.8421 (pm20) REVERT: C 135 LEU cc_start: 0.8084 (tt) cc_final: 0.7871 (tt) REVERT: C 198 PHE cc_start: 0.8949 (m-10) cc_final: 0.8691 (m-10) REVERT: H 46 GLU cc_start: 0.8641 (tt0) cc_final: 0.7985 (tp30) REVERT: H 48 MET cc_start: 0.9447 (mtm) cc_final: 0.8417 (mtp) REVERT: H 150 ASP cc_start: 0.8701 (m-30) cc_final: 0.8465 (m-30) REVERT: H 215 LYS cc_start: 0.8236 (tppt) cc_final: 0.7853 (tptp) REVERT: L 3 GLU cc_start: 0.8807 (tt0) cc_final: 0.8499 (tm-30) REVERT: L 4 LEU cc_start: 0.8742 (mt) cc_final: 0.8298 (mm) REVERT: L 136 LEU cc_start: 0.8545 (mt) cc_final: 0.8242 (mp) REVERT: L 140 ILE cc_start: 0.9424 (mp) cc_final: 0.9042 (mp) REVERT: L 143 PHE cc_start: 0.8944 (p90) cc_final: 0.8147 (p90) REVERT: L 197 CYS cc_start: 0.6912 (t) cc_final: 0.6398 (p) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.0881 time to fit residues: 28.3953 Evaluate side-chains 165 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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: 0.4980 chunk 46 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.067222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.052226 restraints weight = 48384.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.054122 restraints weight = 27624.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.055414 restraints weight = 18306.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.056264 restraints weight = 13535.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.056842 restraints weight = 10924.145| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10939 Z= 0.142 Angle : 0.667 10.192 14930 Z= 0.336 Chirality : 0.045 0.274 1735 Planarity : 0.005 0.044 1862 Dihedral : 6.196 56.740 1745 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.30 (0.23), residues: 1336 helix: 0.67 (0.27), residues: 343 sheet: 0.63 (0.28), residues: 305 loop : -0.14 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 71 TYR 0.030 0.002 TYR L 49 PHE 0.016 0.002 PHE A 298 TRP 0.020 0.002 TRP L 189 HIS 0.007 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00312 (10909) covalent geometry : angle 0.63834 (14856) SS BOND : bond 0.00305 ( 16) SS BOND : angle 2.11859 ( 32) hydrogen bonds : bond 0.04327 ( 483) hydrogen bonds : angle 5.68210 ( 1263) link_ALPHA1-2 : bond 0.00720 ( 1) link_ALPHA1-2 : angle 1.86878 ( 3) link_ALPHA1-3 : bond 0.00785 ( 1) link_ALPHA1-3 : angle 2.30346 ( 3) link_ALPHA1-6 : bond 0.01183 ( 1) link_ALPHA1-6 : angle 1.11805 ( 3) link_BETA1-4 : bond 0.01985 ( 2) link_BETA1-4 : angle 3.63572 ( 6) link_NAG-ASN : bond 0.00779 ( 9) link_NAG-ASN : angle 3.51495 ( 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 215 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8127 (tmm) cc_final: 0.7803 (tmm) REVERT: A 138 LEU cc_start: 0.8929 (mt) cc_final: 0.8510 (mt) REVERT: A 160 LEU cc_start: 0.8575 (pt) cc_final: 0.8317 (tp) REVERT: A 163 ASN cc_start: 0.8314 (m-40) cc_final: 0.7966 (m-40) REVERT: A 313 VAL cc_start: 0.9518 (p) cc_final: 0.9210 (m) REVERT: A 317 TRP cc_start: 0.9238 (t60) cc_final: 0.8746 (t60) REVERT: A 318 LEU cc_start: 0.9704 (mt) cc_final: 0.9432 (pp) REVERT: A 349 GLU cc_start: 0.9326 (tt0) cc_final: 0.8985 (tt0) REVERT: A 458 GLU cc_start: 0.8924 (tt0) cc_final: 0.8237 (tt0) REVERT: A 494 MET cc_start: 0.8702 (ttp) cc_final: 0.8131 (tmm) REVERT: A 579 LEU cc_start: 0.9186 (tp) cc_final: 0.8159 (pp) REVERT: B 106 GLU cc_start: 0.9225 (tt0) cc_final: 0.8736 (pt0) REVERT: C 81 TRP cc_start: 0.8806 (m-90) cc_final: 0.7612 (m100) REVERT: C 92 GLN cc_start: 0.9124 (mm110) cc_final: 0.8901 (mm110) REVERT: C 105 ARG cc_start: 0.9302 (tpp80) cc_final: 0.8996 (tpp80) REVERT: C 116 PHE cc_start: 0.8014 (m-80) cc_final: 0.6857 (m-80) REVERT: C 125 TRP cc_start: 0.7825 (t60) cc_final: 0.7271 (t60) REVERT: C 198 PHE cc_start: 0.9005 (m-10) cc_final: 0.8763 (m-10) REVERT: H 34 ILE cc_start: 0.8903 (mt) cc_final: 0.8692 (mt) REVERT: H 46 GLU cc_start: 0.8577 (tt0) cc_final: 0.7940 (tp30) REVERT: H 48 MET cc_start: 0.9480 (mtm) cc_final: 0.8475 (mtp) REVERT: H 201 ILE cc_start: 0.9298 (tt) cc_final: 0.9034 (mm) REVERT: H 212 LYS cc_start: 0.9152 (tttm) cc_final: 0.8534 (mmtt) REVERT: L 3 GLU cc_start: 0.8739 (tt0) cc_final: 0.8189 (tm-30) REVERT: L 4 LEU cc_start: 0.8695 (mt) cc_final: 0.8079 (tt) REVERT: L 136 LEU cc_start: 0.8855 (mt) cc_final: 0.8444 (mm) REVERT: L 140 ILE cc_start: 0.9430 (mp) cc_final: 0.9123 (mp) REVERT: L 143 PHE cc_start: 0.8928 (p90) cc_final: 0.8185 (p90) REVERT: L 189 TRP cc_start: 0.7988 (t-100) cc_final: 0.7697 (t-100) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.0882 time to fit residues: 28.5094 Evaluate side-chains 171 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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: 3.9990 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 12 optimal weight: 0.0040 chunk 50 optimal weight: 0.0870 overall best weight: 0.2370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN C 103 ASN L 33 HIS L 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.068769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.053683 restraints weight = 47723.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.055598 restraints weight = 27307.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.056898 restraints weight = 18150.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.057705 restraints weight = 13440.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.058365 restraints weight = 10940.204| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10939 Z= 0.125 Angle : 0.666 10.366 14930 Z= 0.331 Chirality : 0.045 0.402 1735 Planarity : 0.005 0.045 1862 Dihedral : 5.917 56.986 1745 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 0.40 (0.23), residues: 1336 helix: 0.75 (0.27), residues: 340 sheet: 0.66 (0.28), residues: 312 loop : -0.07 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 216 TYR 0.028 0.002 TYR L 49 PHE 0.028 0.002 PHE A 238 TRP 0.052 0.002 TRP H 160 HIS 0.007 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00269 (10909) covalent geometry : angle 0.64363 (14856) SS BOND : bond 0.00434 ( 16) SS BOND : angle 1.45176 ( 32) hydrogen bonds : bond 0.04013 ( 483) hydrogen bonds : angle 5.49842 ( 1263) link_ALPHA1-2 : bond 0.00917 ( 1) link_ALPHA1-2 : angle 1.59807 ( 3) link_ALPHA1-3 : bond 0.01147 ( 1) link_ALPHA1-3 : angle 2.43208 ( 3) link_ALPHA1-6 : bond 0.00960 ( 1) link_ALPHA1-6 : angle 1.24168 ( 3) link_BETA1-4 : bond 0.01964 ( 2) link_BETA1-4 : angle 3.47044 ( 6) link_NAG-ASN : bond 0.00620 ( 9) link_NAG-ASN : angle 3.28821 ( 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 223 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8415 (tmm) cc_final: 0.8032 (tmm) REVERT: A 138 LEU cc_start: 0.8979 (mt) cc_final: 0.8410 (mt) REVERT: A 160 LEU cc_start: 0.8478 (pt) cc_final: 0.8234 (tp) REVERT: A 163 ASN cc_start: 0.8320 (m-40) cc_final: 0.7752 (m110) REVERT: A 313 VAL cc_start: 0.9597 (p) cc_final: 0.9225 (m) REVERT: A 318 LEU cc_start: 0.9691 (mt) cc_final: 0.9410 (pp) REVERT: A 349 GLU cc_start: 0.9305 (tt0) cc_final: 0.8963 (tt0) REVERT: A 458 GLU cc_start: 0.8947 (tt0) cc_final: 0.8360 (tt0) REVERT: A 494 MET cc_start: 0.8674 (ttp) cc_final: 0.8271 (tmm) REVERT: A 579 LEU cc_start: 0.9224 (tp) cc_final: 0.8222 (pp) REVERT: A 640 GLN cc_start: 0.8872 (tt0) cc_final: 0.8143 (mt0) REVERT: B 88 PHE cc_start: 0.9156 (t80) cc_final: 0.8888 (t80) REVERT: B 106 GLU cc_start: 0.9205 (tt0) cc_final: 0.8731 (pt0) REVERT: C 81 TRP cc_start: 0.8737 (m-90) cc_final: 0.7514 (m100) REVERT: C 92 GLN cc_start: 0.9184 (mm110) cc_final: 0.8912 (mm110) REVERT: C 105 ARG cc_start: 0.9263 (tpp80) cc_final: 0.8964 (tpp80) REVERT: C 116 PHE cc_start: 0.8053 (m-80) cc_final: 0.7129 (m-80) REVERT: C 125 TRP cc_start: 0.7706 (t60) cc_final: 0.7123 (t60) REVERT: C 198 PHE cc_start: 0.9003 (m-10) cc_final: 0.8744 (m-10) REVERT: H 46 GLU cc_start: 0.8656 (tt0) cc_final: 0.8080 (tp30) REVERT: H 48 MET cc_start: 0.9553 (mtm) cc_final: 0.8429 (mtp) REVERT: H 69 MET cc_start: 0.7362 (mmp) cc_final: 0.6826 (mmm) REVERT: H 149 LYS cc_start: 0.8310 (ptmm) cc_final: 0.8085 (ptmm) REVERT: H 150 ASP cc_start: 0.8575 (m-30) cc_final: 0.8152 (m-30) REVERT: H 201 ILE cc_start: 0.9148 (tt) cc_final: 0.8943 (mm) REVERT: H 212 LYS cc_start: 0.9207 (tttm) cc_final: 0.8655 (mmtt) REVERT: L 3 GLU cc_start: 0.8565 (tt0) cc_final: 0.8041 (tm-30) REVERT: L 4 LEU cc_start: 0.8711 (mt) cc_final: 0.8102 (tt) REVERT: L 31 ASN cc_start: 0.8612 (t0) cc_final: 0.7997 (t0) REVERT: L 49 TYR cc_start: 0.8718 (m-10) cc_final: 0.8450 (m-10) REVERT: L 136 LEU cc_start: 0.8988 (mt) cc_final: 0.8576 (mm) REVERT: L 140 ILE cc_start: 0.9523 (mp) cc_final: 0.9098 (mp) REVERT: L 143 PHE cc_start: 0.8978 (p90) cc_final: 0.8200 (p90) REVERT: L 189 TRP cc_start: 0.7926 (t-100) cc_final: 0.7630 (t-100) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.0868 time to fit residues: 28.9585 Evaluate side-chains 173 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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: 0.7980 chunk 19 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 52 optimal weight: 0.0670 chunk 61 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.068626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.053581 restraints weight = 48185.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.055544 restraints weight = 27615.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.056876 restraints weight = 18238.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.057771 restraints weight = 13468.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.058405 restraints weight = 10821.491| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10939 Z= 0.125 Angle : 0.643 10.261 14930 Z= 0.324 Chirality : 0.044 0.371 1735 Planarity : 0.005 0.042 1862 Dihedral : 5.842 56.086 1745 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.41 (0.23), residues: 1336 helix: 0.83 (0.27), residues: 340 sheet: 0.60 (0.28), residues: 312 loop : -0.07 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 279 TYR 0.015 0.002 TYR H 108 PHE 0.021 0.002 PHE A 298 TRP 0.022 0.002 TRP A 317 HIS 0.007 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00270 (10909) covalent geometry : angle 0.62174 (14856) SS BOND : bond 0.00423 ( 16) SS BOND : angle 1.23038 ( 32) hydrogen bonds : bond 0.03914 ( 483) hydrogen bonds : angle 5.39903 ( 1263) link_ALPHA1-2 : bond 0.00748 ( 1) link_ALPHA1-2 : angle 1.55110 ( 3) link_ALPHA1-3 : bond 0.00909 ( 1) link_ALPHA1-3 : angle 2.37688 ( 3) link_ALPHA1-6 : bond 0.01049 ( 1) link_ALPHA1-6 : angle 1.14466 ( 3) link_BETA1-4 : bond 0.01918 ( 2) link_BETA1-4 : angle 3.51628 ( 6) link_NAG-ASN : bond 0.00609 ( 9) link_NAG-ASN : angle 3.23091 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1771.28 seconds wall clock time: 31 minutes 30.27 seconds (1890.27 seconds total)