Starting phenix.real_space_refine on Tue Jul 29 04:10:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c5v_7344/07_2025/6c5v_7344.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c5v_7344/07_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_7344/07_2025/6c5v_7344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c5v_7344/07_2025/6c5v_7344.map" model { file = "/net/cci-nas-00/data/ceres_data/6c5v_7344/07_2025/6c5v_7344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c5v_7344/07_2025/6c5v_7344.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.95, per 1000 atoms: 0.65 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: 2.98 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.76 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: 3.84 Time building geometry restraints manager: 3.39 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.970 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (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 TRP 0.036 0.006 TRP H 160 HIS 0.006 0.001 HIS A 239 PHE 0.029 0.005 PHE L 101 TYR 0.037 0.005 TYR L 99 ARG 0.007 0.001 ARG H 101 Details of bonding type rmsd link_NAG-ASN : bond 0.02766 ( 9) link_NAG-ASN : angle 1.96292 ( 27) 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_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) hydrogen bonds : bond 0.17846 ( 483) hydrogen bonds : angle 7.70787 ( 1263) SS BOND : bond 0.02407 ( 16) SS BOND : angle 3.87487 ( 32) covalent geometry : bond 0.01346 (10909) covalent geometry : angle 1.30377 (14856) *********************** 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 : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.8735 (tt) cc_final: 0.8475 (mp) REVERT: A 73 LYS cc_start: 0.9077 (pttt) cc_final: 0.8853 (ttpt) REVERT: A 137 MET cc_start: 0.8720 (tpt) cc_final: 0.8476 (tmm) REVERT: A 217 THR cc_start: 0.9416 (m) cc_final: 0.9054 (t) REVERT: A 283 LEU cc_start: 0.9224 (mt) cc_final: 0.8974 (mt) REVERT: A 286 GLU cc_start: 0.8477 (tt0) cc_final: 0.8257 (tm-30) REVERT: A 317 TRP cc_start: 0.9231 (t60) cc_final: 0.8607 (t60) REVERT: A 318 LEU cc_start: 0.9669 (mt) cc_final: 0.9264 (mt) REVERT: A 384 PRO cc_start: 0.8738 (Cg_endo) cc_final: 0.8311 (Cg_exo) REVERT: A 404 TYR cc_start: 0.8521 (t80) cc_final: 0.8318 (t80) REVERT: A 413 LEU cc_start: 0.9196 (mt) cc_final: 0.8803 (tp) REVERT: A 417 MET cc_start: 0.8654 (mtt) cc_final: 0.8027 (mmm) REVERT: A 466 LEU cc_start: 0.8762 (mt) cc_final: 0.8534 (tt) REVERT: A 537 ARG cc_start: 0.8321 (mmt-90) cc_final: 0.8083 (mtt180) REVERT: A 551 THR cc_start: 0.9436 (m) cc_final: 0.8891 (p) REVERT: A 582 VAL cc_start: 0.9275 (t) cc_final: 0.8977 (t) REVERT: A 614 PHE cc_start: 0.8703 (m-80) cc_final: 0.8141 (m-80) REVERT: B 81 ASN cc_start: 0.8692 (t0) cc_final: 0.7772 (p0) REVERT: B 84 ASN cc_start: 0.9456 (m-40) cc_final: 0.9100 (m-40) REVERT: B 89 PHE cc_start: 0.9082 (m-80) cc_final: 0.8544 (m-80) REVERT: B 106 GLU cc_start: 0.9335 (tt0) cc_final: 0.8836 (tm-30) REVERT: B 115 TYR cc_start: 0.7975 (t80) cc_final: 0.7448 (t80) REVERT: B 128 LEU cc_start: 0.8441 (mt) cc_final: 0.8127 (mm) REVERT: C 81 TRP cc_start: 0.8456 (m-90) cc_final: 0.8210 (m100) REVERT: C 98 ASN cc_start: 0.0921 (OUTLIER) cc_final: -0.0613 (t0) REVERT: C 116 PHE cc_start: 0.8122 (m-80) cc_final: 0.7467 (m-80) REVERT: C 155 ASN cc_start: 0.7223 (m-40) cc_final: 0.7002 (m-40) REVERT: C 169 VAL cc_start: 0.7855 (t) cc_final: 0.7646 (p) REVERT: C 171 GLU cc_start: 0.8326 (mm-30) cc_final: 0.6783 (tm-30) REVERT: C 182 PHE cc_start: 0.7768 (m-80) cc_final: 0.7554 (m-80) REVERT: C 188 PHE cc_start: 0.8755 (m-80) cc_final: 0.8509 (m-80) REVERT: C 211 LEU cc_start: 0.9069 (mt) cc_final: 0.8585 (mm) REVERT: H 25 SER cc_start: 0.7949 (t) cc_final: 0.7677 (m) REVERT: H 32 PHE cc_start: 0.8798 (m-80) cc_final: 0.8303 (m-80) REVERT: H 69 MET cc_start: 0.7626 (mtm) cc_final: 0.6946 (mtm) REVERT: H 98 MET cc_start: 0.8100 (ttt) cc_final: 0.5716 (tpt) REVERT: H 160 TRP cc_start: 0.8302 (m100) cc_final: 0.7948 (m100) REVERT: H 165 LEU cc_start: 0.8342 (tp) cc_final: 0.7845 (mm) REVERT: H 215 LYS cc_start: 0.7945 (tppt) cc_final: 0.7733 (tptp) REVERT: L 3 GLU cc_start: 0.8691 (tt0) cc_final: 0.8275 (tm-30) REVERT: L 4 LEU cc_start: 0.8856 (mt) cc_final: 0.8630 (tt) REVERT: L 20 ILE cc_start: 0.9481 (mm) cc_final: 0.9275 (tp) REVERT: L 49 TYR cc_start: 0.8794 (m-80) cc_final: 0.7943 (m-80) REVERT: L 75 SER cc_start: 0.8572 (t) cc_final: 0.7781 (m) REVERT: L 84 ASP cc_start: 0.8821 (m-30) cc_final: 0.8545 (m-30) REVERT: L 99 TYR cc_start: 0.7893 (m-80) cc_final: 0.7300 (m-80) REVERT: L 121 LEU cc_start: 0.8511 (tp) cc_final: 0.8203 (tt) REVERT: L 136 LEU cc_start: 0.8919 (mt) cc_final: 0.8570 (mm) REVERT: L 138 CYS cc_start: 0.7638 (t) cc_final: 0.6899 (t) REVERT: L 143 PHE cc_start: 0.8874 (p90) cc_final: 0.8357 (p90) REVERT: L 174 ASN cc_start: 0.8797 (t0) cc_final: 0.8476 (t0) outliers start: 5 outliers final: 1 residues processed: 398 average time/residue: 0.2420 time to fit residues: 134.0254 Evaluate side-chains 236 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 77 optimal weight: 0.0870 chunk 120 optimal weight: 1.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN L 88 GLN L 96 HIS L 192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.056653 restraints weight = 45182.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.058777 restraints weight = 25583.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.060214 restraints weight = 16915.913| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10939 Z= 0.159 Angle : 0.688 11.189 14930 Z= 0.357 Chirality : 0.045 0.350 1735 Planarity : 0.005 0.041 1862 Dihedral : 8.222 84.684 1745 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.22), residues: 1336 helix: 0.67 (0.27), residues: 343 sheet: 0.93 (0.28), residues: 327 loop : 0.06 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 36 HIS 0.007 0.001 HIS H 206 PHE 0.026 0.002 PHE L 101 TYR 0.028 0.002 TYR C 185 ARG 0.005 0.001 ARG A 418 Details of bonding type rmsd link_NAG-ASN : bond 0.01199 ( 9) link_NAG-ASN : angle 3.58936 ( 27) link_ALPHA1-6 : bond 0.00990 ( 1) link_ALPHA1-6 : angle 1.55189 ( 3) link_BETA1-4 : bond 0.02028 ( 2) link_BETA1-4 : angle 3.42820 ( 6) link_ALPHA1-2 : bond 0.00398 ( 1) link_ALPHA1-2 : angle 1.50432 ( 3) link_ALPHA1-3 : bond 0.00664 ( 1) link_ALPHA1-3 : angle 2.06495 ( 3) hydrogen bonds : bond 0.05932 ( 483) hydrogen bonds : angle 5.83196 ( 1263) SS BOND : bond 0.00396 ( 16) SS BOND : angle 1.22380 ( 32) covalent geometry : bond 0.00341 (10909) covalent geometry : angle 0.66520 (14856) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.9400 (tp) cc_final: 0.9173 (tp) REVERT: A 137 MET cc_start: 0.8367 (tpt) cc_final: 0.8091 (tpp) REVERT: A 138 LEU cc_start: 0.9291 (mt) cc_final: 0.8975 (mt) REVERT: A 217 THR cc_start: 0.9382 (m) cc_final: 0.9090 (t) REVERT: A 283 LEU cc_start: 0.8947 (mt) cc_final: 0.8620 (mt) REVERT: A 317 TRP cc_start: 0.9025 (t60) cc_final: 0.8408 (t60) REVERT: A 318 LEU cc_start: 0.9513 (mt) cc_final: 0.9159 (mt) REVERT: A 349 GLU cc_start: 0.9285 (tt0) cc_final: 0.8954 (tt0) REVERT: A 413 LEU cc_start: 0.8836 (mt) cc_final: 0.8568 (tp) REVERT: A 417 MET cc_start: 0.8360 (mtt) cc_final: 0.8004 (mmm) REVERT: A 458 GLU cc_start: 0.8490 (tt0) cc_final: 0.7450 (tt0) REVERT: A 537 ARG cc_start: 0.8198 (mmt-90) cc_final: 0.7926 (mtt180) REVERT: A 551 THR cc_start: 0.9362 (m) cc_final: 0.8909 (p) REVERT: A 582 VAL cc_start: 0.9183 (t) cc_final: 0.8840 (t) REVERT: A 614 PHE cc_start: 0.8597 (m-80) cc_final: 0.8237 (m-80) REVERT: A 635 THR cc_start: 0.9236 (p) cc_final: 0.8898 (t) REVERT: A 649 PHE cc_start: 0.8326 (m-80) cc_final: 0.8013 (m-80) REVERT: B 81 ASN cc_start: 0.8844 (t0) cc_final: 0.8468 (t0) REVERT: B 84 ASN cc_start: 0.9295 (m-40) cc_final: 0.9016 (m-40) REVERT: B 89 PHE cc_start: 0.9032 (m-80) cc_final: 0.8122 (m-80) REVERT: B 106 GLU cc_start: 0.9242 (tt0) cc_final: 0.8760 (tm-30) REVERT: B 112 GLU cc_start: 0.9215 (pt0) cc_final: 0.8887 (pt0) REVERT: B 128 LEU cc_start: 0.8346 (mt) cc_final: 0.7964 (mm) REVERT: C 73 ASP cc_start: 0.6637 (t0) cc_final: 0.5922 (t0) REVERT: C 81 TRP cc_start: 0.8418 (m-90) cc_final: 0.8042 (m100) REVERT: C 116 PHE cc_start: 0.8258 (m-80) cc_final: 0.7288 (m-80) REVERT: C 171 GLU cc_start: 0.8127 (mm-30) cc_final: 0.6696 (tm-30) REVERT: C 182 PHE cc_start: 0.7852 (m-80) cc_final: 0.7349 (m-80) REVERT: C 198 PHE cc_start: 0.8886 (m-10) cc_final: 0.8586 (m-10) REVERT: C 206 HIS cc_start: 0.7803 (p-80) cc_final: 0.7596 (p-80) REVERT: H 32 PHE cc_start: 0.8642 (m-80) cc_final: 0.7842 (m-80) REVERT: H 80 MET cc_start: 0.8388 (tmm) cc_final: 0.8187 (tmm) REVERT: H 98 MET cc_start: 0.6421 (ttt) cc_final: 0.5820 (tpt) REVERT: H 101 ARG cc_start: 0.8405 (ptp-170) cc_final: 0.8031 (ptp-170) REVERT: L 3 GLU cc_start: 0.8623 (tt0) cc_final: 0.8225 (tm-30) REVERT: L 4 LEU cc_start: 0.8788 (mt) cc_final: 0.8555 (tp) REVERT: L 20 ILE cc_start: 0.9338 (mm) cc_final: 0.9045 (pt) REVERT: L 46 VAL cc_start: 0.9458 (m) cc_final: 0.9213 (p) REVERT: L 57 ILE cc_start: 0.7627 (mp) cc_final: 0.7150 (mp) REVERT: L 84 ASP cc_start: 0.8970 (m-30) cc_final: 0.8618 (m-30) REVERT: L 99 TYR cc_start: 0.7766 (m-80) cc_final: 0.6851 (m-80) REVERT: L 128 GLU cc_start: 0.9278 (tp30) cc_final: 0.8772 (tp30) REVERT: L 136 LEU cc_start: 0.8816 (mt) cc_final: 0.8489 (mm) REVERT: L 143 PHE cc_start: 0.8859 (p90) cc_final: 0.8291 (p90) REVERT: L 174 ASN cc_start: 0.8601 (t0) cc_final: 0.8175 (t0) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2315 time to fit residues: 101.9267 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 : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 88 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** B 103 HIS C 103 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.067609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.052425 restraints weight = 48202.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.054377 restraints weight = 27129.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.055732 restraints weight = 17887.183| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10939 Z= 0.239 Angle : 0.728 10.395 14930 Z= 0.378 Chirality : 0.046 0.245 1735 Planarity : 0.006 0.046 1862 Dihedral : 7.769 78.463 1745 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1336 helix: 0.34 (0.26), residues: 343 sheet: 0.65 (0.27), residues: 329 loop : -0.16 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 189 HIS 0.008 0.002 HIS A 407 PHE 0.036 0.003 PHE L 122 TYR 0.022 0.002 TYR C 185 ARG 0.011 0.001 ARG L 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 9) link_NAG-ASN : angle 3.12940 ( 27) link_ALPHA1-6 : bond 0.01469 ( 1) link_ALPHA1-6 : angle 0.91847 ( 3) link_BETA1-4 : bond 0.02098 ( 2) link_BETA1-4 : angle 3.80969 ( 6) link_ALPHA1-2 : bond 0.00054 ( 1) link_ALPHA1-2 : angle 1.85120 ( 3) link_ALPHA1-3 : bond 0.00308 ( 1) link_ALPHA1-3 : angle 1.86512 ( 3) hydrogen bonds : bond 0.05385 ( 483) hydrogen bonds : angle 5.80872 ( 1263) SS BOND : bond 0.00456 ( 16) SS BOND : angle 1.22016 ( 32) covalent geometry : bond 0.00504 (10909) covalent geometry : angle 0.71044 (14856) *********************** 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 246 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9133 (mtt) cc_final: 0.8871 (tpp) REVERT: A 138 LEU cc_start: 0.9383 (mt) cc_final: 0.8855 (mt) REVERT: A 160 LEU cc_start: 0.8783 (pt) cc_final: 0.8158 (tp) REVERT: A 217 THR cc_start: 0.9387 (m) cc_final: 0.9135 (t) REVERT: A 249 MET cc_start: 0.8910 (ttp) cc_final: 0.8597 (ttm) REVERT: A 317 TRP cc_start: 0.9189 (t60) cc_final: 0.8609 (t60) REVERT: A 318 LEU cc_start: 0.9689 (mt) cc_final: 0.9275 (mt) REVERT: A 349 GLU cc_start: 0.9338 (tt0) cc_final: 0.9010 (tt0) REVERT: A 413 LEU cc_start: 0.8782 (mt) cc_final: 0.8550 (tp) REVERT: A 458 GLU cc_start: 0.8651 (tt0) cc_final: 0.7756 (tt0) REVERT: A 544 ILE cc_start: 0.9119 (mt) cc_final: 0.8841 (mt) REVERT: A 551 THR cc_start: 0.9404 (m) cc_final: 0.9004 (p) REVERT: A 614 PHE cc_start: 0.8750 (m-80) cc_final: 0.8392 (m-10) REVERT: A 619 LEU cc_start: 0.9526 (tp) cc_final: 0.9309 (tp) REVERT: B 89 PHE cc_start: 0.9048 (m-80) cc_final: 0.8206 (m-80) REVERT: B 106 GLU cc_start: 0.9378 (tt0) cc_final: 0.8781 (tm-30) REVERT: B 128 LEU cc_start: 0.8614 (mt) cc_final: 0.8364 (mm) REVERT: C 81 TRP cc_start: 0.8909 (m-90) cc_final: 0.8113 (m100) REVERT: C 92 GLN cc_start: 0.8862 (mm110) cc_final: 0.8635 (mm110) REVERT: C 116 PHE cc_start: 0.8201 (m-80) cc_final: 0.7367 (m-80) REVERT: C 182 PHE cc_start: 0.8059 (m-80) cc_final: 0.7428 (m-80) REVERT: C 198 PHE cc_start: 0.8906 (m-10) cc_final: 0.8626 (m-10) REVERT: H 48 MET cc_start: 0.9307 (mtm) cc_final: 0.8506 (mpp) REVERT: H 98 MET cc_start: 0.6887 (ttt) cc_final: 0.6531 (tpt) REVERT: H 109 TRP cc_start: 0.8757 (m100) cc_final: 0.7786 (m-10) REVERT: H 215 LYS cc_start: 0.8205 (tppt) cc_final: 0.7668 (tptp) REVERT: L 3 GLU cc_start: 0.8735 (tt0) cc_final: 0.8351 (tm-30) REVERT: L 4 LEU cc_start: 0.8760 (mt) cc_final: 0.8429 (tp) REVERT: L 20 ILE cc_start: 0.9405 (mm) cc_final: 0.9127 (pt) REVERT: L 84 ASP cc_start: 0.8997 (m-30) cc_final: 0.8766 (m-30) REVERT: L 99 TYR cc_start: 0.8508 (m-80) cc_final: 0.6218 (m-10) REVERT: L 136 LEU cc_start: 0.8836 (mt) cc_final: 0.8410 (mm) REVERT: L 143 PHE cc_start: 0.9056 (p90) cc_final: 0.8157 (p90) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2093 time to fit residues: 76.0593 Evaluate side-chains 185 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN B 30 HIS L 31 ASN L 192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.068686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.053085 restraints weight = 47112.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.055053 restraints weight = 26999.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.056411 restraints weight = 18036.725| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10939 Z= 0.143 Angle : 0.641 10.457 14930 Z= 0.325 Chirality : 0.043 0.263 1735 Planarity : 0.005 0.052 1862 Dihedral : 7.283 70.566 1745 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1336 helix: 0.91 (0.28), residues: 333 sheet: 0.68 (0.27), residues: 326 loop : 0.01 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 160 HIS 0.007 0.001 HIS A 239 PHE 0.024 0.002 PHE C 88 TYR 0.019 0.002 TYR L 195 ARG 0.006 0.001 ARG L 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 9) link_NAG-ASN : angle 3.57738 ( 27) link_ALPHA1-6 : bond 0.01165 ( 1) link_ALPHA1-6 : angle 1.24501 ( 3) link_BETA1-4 : bond 0.02105 ( 2) link_BETA1-4 : angle 3.44152 ( 6) link_ALPHA1-2 : bond 0.00311 ( 1) link_ALPHA1-2 : angle 1.65370 ( 3) link_ALPHA1-3 : bond 0.00345 ( 1) link_ALPHA1-3 : angle 2.09420 ( 3) hydrogen bonds : bond 0.04618 ( 483) hydrogen bonds : angle 5.45373 ( 1263) SS BOND : bond 0.00373 ( 16) SS BOND : angle 1.07358 ( 32) covalent geometry : bond 0.00307 (10909) covalent geometry : angle 0.61704 (14856) *********************** 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 245 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.222 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 68 MET cc_start: 0.8539 (tpp) cc_final: 0.8301 (mmm) REVERT: A 138 LEU cc_start: 0.9310 (mt) cc_final: 0.9042 (mt) REVERT: A 160 LEU cc_start: 0.8460 (pt) cc_final: 0.8053 (tp) REVERT: A 163 ASN cc_start: 0.8432 (m110) cc_final: 0.8131 (m-40) REVERT: A 217 THR cc_start: 0.9387 (m) cc_final: 0.9127 (t) REVERT: A 226 LEU cc_start: 0.9066 (mt) cc_final: 0.8790 (mt) REVERT: A 317 TRP cc_start: 0.9125 (t60) cc_final: 0.8618 (t60) REVERT: A 318 LEU cc_start: 0.9619 (mt) cc_final: 0.9403 (mt) REVERT: A 349 GLU cc_start: 0.9251 (tt0) cc_final: 0.8767 (tt0) REVERT: A 451 THR cc_start: 0.9502 (m) cc_final: 0.9279 (p) REVERT: A 458 GLU cc_start: 0.8747 (tt0) cc_final: 0.7813 (tt0) REVERT: A 482 LEU cc_start: 0.9326 (mt) cc_final: 0.9114 (mt) REVERT: A 486 LEU cc_start: 0.7467 (tp) cc_final: 0.7162 (tp) REVERT: A 544 ILE cc_start: 0.9179 (mt) cc_final: 0.8839 (mt) REVERT: A 551 THR cc_start: 0.9379 (m) cc_final: 0.8973 (p) REVERT: A 582 VAL cc_start: 0.9114 (t) cc_final: 0.8847 (t) REVERT: A 614 PHE cc_start: 0.8835 (m-80) cc_final: 0.8581 (m-10) REVERT: B 81 ASN cc_start: 0.8929 (t0) cc_final: 0.8311 (t0) REVERT: B 89 PHE cc_start: 0.8979 (m-80) cc_final: 0.8193 (m-80) REVERT: B 106 GLU cc_start: 0.9355 (tt0) cc_final: 0.8777 (tm-30) REVERT: B 107 LEU cc_start: 0.9560 (tp) cc_final: 0.9356 (tp) REVERT: B 128 LEU cc_start: 0.8607 (mt) cc_final: 0.8333 (mm) REVERT: C 81 TRP cc_start: 0.8784 (m-90) cc_final: 0.7985 (m100) REVERT: C 92 GLN cc_start: 0.8951 (mm110) cc_final: 0.8667 (mm110) REVERT: C 105 ARG cc_start: 0.9377 (tpp80) cc_final: 0.9049 (tpp80) REVERT: C 134 GLU cc_start: 0.8875 (pm20) cc_final: 0.8635 (pm20) REVERT: C 182 PHE cc_start: 0.8005 (m-80) cc_final: 0.7371 (m-80) REVERT: C 198 PHE cc_start: 0.8969 (m-10) cc_final: 0.8737 (m-10) REVERT: H 25 SER cc_start: 0.8135 (t) cc_final: 0.7822 (m) REVERT: H 48 MET cc_start: 0.9344 (mtm) cc_final: 0.8386 (mtp) REVERT: H 98 MET cc_start: 0.6872 (ttt) cc_final: 0.6360 (tpt) REVERT: H 104 PHE cc_start: 0.8307 (m-10) cc_final: 0.7730 (m-80) REVERT: H 212 LYS cc_start: 0.9056 (tttp) cc_final: 0.8022 (mmtt) REVERT: H 215 LYS cc_start: 0.8309 (tppt) cc_final: 0.7930 (tptp) REVERT: L 3 GLU cc_start: 0.8696 (tt0) cc_final: 0.8361 (tm-30) REVERT: L 4 LEU cc_start: 0.8660 (mt) cc_final: 0.8264 (tt) REVERT: L 49 TYR cc_start: 0.8902 (m-10) cc_final: 0.8362 (m-10) REVERT: L 84 ASP cc_start: 0.8946 (m-30) cc_final: 0.8665 (m-30) REVERT: L 86 TYR cc_start: 0.8489 (m-80) cc_final: 0.8099 (m-10) REVERT: L 99 TYR cc_start: 0.8265 (m-80) cc_final: 0.5809 (m-10) REVERT: L 128 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8213 (mm-30) REVERT: L 136 LEU cc_start: 0.8601 (mt) cc_final: 0.8347 (mm) REVERT: L 143 PHE cc_start: 0.9060 (p90) cc_final: 0.8231 (p90) REVERT: L 182 LEU cc_start: 0.8982 (tt) cc_final: 0.8747 (tt) REVERT: L 184 LEU cc_start: 0.7889 (mt) cc_final: 0.7645 (tp) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1998 time to fit residues: 72.8410 Evaluate side-chains 189 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 109 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 112 optimal weight: 0.0060 chunk 1 optimal weight: 8.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS C 206 HIS H 54 ASN L 192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.051845 restraints weight = 48104.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.053773 restraints weight = 27849.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.055095 restraints weight = 18642.178| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10939 Z= 0.170 Angle : 0.659 11.274 14930 Z= 0.332 Chirality : 0.043 0.247 1735 Planarity : 0.005 0.044 1862 Dihedral : 6.977 62.525 1745 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.09 % Allowed : 1.72 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.23), residues: 1336 helix: 0.99 (0.28), residues: 329 sheet: 0.84 (0.28), residues: 314 loop : -0.11 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 189 HIS 0.005 0.001 HIS A 528 PHE 0.028 0.002 PHE B 88 TYR 0.025 0.002 TYR L 144 ARG 0.003 0.000 ARG A 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00614 ( 9) link_NAG-ASN : angle 3.08672 ( 27) link_ALPHA1-6 : bond 0.01046 ( 1) link_ALPHA1-6 : angle 1.15215 ( 3) link_BETA1-4 : bond 0.02179 ( 2) link_BETA1-4 : angle 3.60110 ( 6) link_ALPHA1-2 : bond 0.00347 ( 1) link_ALPHA1-2 : angle 1.72580 ( 3) link_ALPHA1-3 : bond 0.00231 ( 1) link_ALPHA1-3 : angle 2.07844 ( 3) hydrogen bonds : bond 0.04479 ( 483) hydrogen bonds : angle 5.53949 ( 1263) SS BOND : bond 0.00385 ( 16) SS BOND : angle 1.45829 ( 32) covalent geometry : bond 0.00372 (10909) covalent geometry : angle 0.63832 (14856) *********************** 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 233 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8676 (pt) cc_final: 0.8038 (tp) REVERT: A 163 ASN cc_start: 0.8211 (m-40) cc_final: 0.7944 (m-40) REVERT: A 217 THR cc_start: 0.9296 (m) cc_final: 0.9031 (t) REVERT: A 226 LEU cc_start: 0.8984 (mt) cc_final: 0.8734 (mt) REVERT: A 317 TRP cc_start: 0.9133 (t60) cc_final: 0.8609 (t60) REVERT: A 318 LEU cc_start: 0.9709 (mt) cc_final: 0.9335 (mt) REVERT: A 349 GLU cc_start: 0.9249 (tt0) cc_final: 0.8817 (tt0) REVERT: A 356 MET cc_start: 0.8348 (tmm) cc_final: 0.8111 (ppp) REVERT: A 399 VAL cc_start: 0.9520 (t) cc_final: 0.9309 (t) REVERT: A 401 LEU cc_start: 0.9568 (tp) cc_final: 0.9152 (pp) REVERT: A 458 GLU cc_start: 0.8700 (tt0) cc_final: 0.7848 (tt0) REVERT: A 551 THR cc_start: 0.9345 (m) cc_final: 0.8944 (p) REVERT: A 619 LEU cc_start: 0.9604 (tp) cc_final: 0.9403 (tp) REVERT: B 88 PHE cc_start: 0.9307 (t80) cc_final: 0.8862 (t80) REVERT: B 89 PHE cc_start: 0.9055 (m-80) cc_final: 0.8378 (m-80) REVERT: B 93 LEU cc_start: 0.9632 (mt) cc_final: 0.9428 (mt) REVERT: B 100 LEU cc_start: 0.9046 (mt) cc_final: 0.8611 (mt) REVERT: B 106 GLU cc_start: 0.9298 (tt0) cc_final: 0.8718 (tm-30) REVERT: B 107 LEU cc_start: 0.9566 (tp) cc_final: 0.9359 (tp) REVERT: C 73 ASP cc_start: 0.7755 (t0) cc_final: 0.7520 (t0) REVERT: C 81 TRP cc_start: 0.8826 (m-90) cc_final: 0.7922 (m100) REVERT: C 92 GLN cc_start: 0.9007 (mm110) cc_final: 0.8687 (mm110) REVERT: C 105 ARG cc_start: 0.9383 (tpp80) cc_final: 0.9027 (tpp80) REVERT: C 171 GLU cc_start: 0.8082 (mm-30) cc_final: 0.6950 (tm-30) REVERT: H 25 SER cc_start: 0.8039 (t) cc_final: 0.7754 (m) REVERT: H 46 GLU cc_start: 0.8374 (tt0) cc_final: 0.7884 (tp30) REVERT: H 48 MET cc_start: 0.9311 (mtm) cc_final: 0.8397 (mtp) REVERT: H 98 MET cc_start: 0.7003 (ttt) cc_final: 0.6488 (tpt) REVERT: H 212 LYS cc_start: 0.9202 (tttp) cc_final: 0.8398 (mmtt) REVERT: H 215 LYS cc_start: 0.8401 (tppt) cc_final: 0.8034 (ttpt) REVERT: L 3 GLU cc_start: 0.8751 (tt0) cc_final: 0.8207 (tm-30) REVERT: L 4 LEU cc_start: 0.8694 (mt) cc_final: 0.8267 (tp) REVERT: L 49 TYR cc_start: 0.8804 (m-10) cc_final: 0.8072 (m-10) REVERT: L 84 ASP cc_start: 0.8938 (m-30) cc_final: 0.8703 (m-30) REVERT: L 86 TYR cc_start: 0.8535 (m-80) cc_final: 0.8160 (m-80) REVERT: L 99 TYR cc_start: 0.8449 (m-80) cc_final: 0.6029 (m-10) REVERT: L 136 LEU cc_start: 0.8589 (mt) cc_final: 0.8218 (mm) REVERT: L 143 PHE cc_start: 0.9022 (p90) cc_final: 0.8286 (p90) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.2051 time to fit residues: 71.0805 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 : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 HIS ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS C 103 ASN L 25 HIS ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 192 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.051830 restraints weight = 48220.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.053757 restraints weight = 27495.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.055073 restraints weight = 18354.098| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10939 Z= 0.164 Angle : 0.646 10.140 14930 Z= 0.328 Chirality : 0.043 0.247 1735 Planarity : 0.005 0.044 1862 Dihedral : 6.652 56.592 1745 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.22), residues: 1336 helix: 0.88 (0.27), residues: 338 sheet: 0.73 (0.28), residues: 320 loop : -0.13 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 160 HIS 0.005 0.001 HIS A 528 PHE 0.027 0.002 PHE A 232 TYR 0.017 0.002 TYR C 136 ARG 0.003 0.000 ARG A 418 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 9) link_NAG-ASN : angle 3.15064 ( 27) link_ALPHA1-6 : bond 0.01103 ( 1) link_ALPHA1-6 : angle 1.14968 ( 3) link_BETA1-4 : bond 0.02163 ( 2) link_BETA1-4 : angle 3.62498 ( 6) link_ALPHA1-2 : bond 0.00480 ( 1) link_ALPHA1-2 : angle 1.82110 ( 3) link_ALPHA1-3 : bond 0.00488 ( 1) link_ALPHA1-3 : angle 2.33669 ( 3) hydrogen bonds : bond 0.04392 ( 483) hydrogen bonds : angle 5.46698 ( 1263) SS BOND : bond 0.00508 ( 16) SS BOND : angle 1.20242 ( 32) covalent geometry : bond 0.00353 (10909) covalent geometry : angle 0.62506 (14856) *********************** 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 231 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.8567 (tpp) cc_final: 0.8299 (mmm) REVERT: A 138 LEU cc_start: 0.9083 (mt) cc_final: 0.8475 (mt) REVERT: A 160 LEU cc_start: 0.8690 (pt) cc_final: 0.8101 (tp) REVERT: A 317 TRP cc_start: 0.9140 (t60) cc_final: 0.8620 (t60) REVERT: A 318 LEU cc_start: 0.9731 (mt) cc_final: 0.9369 (mt) REVERT: A 349 GLU cc_start: 0.9249 (tt0) cc_final: 0.8722 (tt0) REVERT: A 356 MET cc_start: 0.8386 (tmm) cc_final: 0.8161 (ppp) REVERT: A 399 VAL cc_start: 0.9511 (t) cc_final: 0.9309 (t) REVERT: A 401 LEU cc_start: 0.9510 (tp) cc_final: 0.9124 (pp) REVERT: A 451 THR cc_start: 0.9540 (m) cc_final: 0.9304 (p) REVERT: A 458 GLU cc_start: 0.8706 (tt0) cc_final: 0.7847 (tt0) REVERT: A 482 LEU cc_start: 0.9404 (mt) cc_final: 0.9137 (mt) REVERT: A 494 MET cc_start: 0.8383 (ttm) cc_final: 0.8155 (ttm) REVERT: A 544 ILE cc_start: 0.9237 (mt) cc_final: 0.8934 (mt) REVERT: B 81 ASN cc_start: 0.8754 (t0) cc_final: 0.8260 (t0) REVERT: B 88 PHE cc_start: 0.9274 (t80) cc_final: 0.8903 (t80) REVERT: B 106 GLU cc_start: 0.9304 (tt0) cc_final: 0.8695 (tm-30) REVERT: B 107 LEU cc_start: 0.9530 (tp) cc_final: 0.9298 (tp) REVERT: C 70 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8704 (mm-30) REVERT: C 73 ASP cc_start: 0.8086 (t0) cc_final: 0.7826 (t0) REVERT: C 81 TRP cc_start: 0.8858 (m-90) cc_final: 0.7924 (m100) REVERT: C 92 GLN cc_start: 0.9000 (mm110) cc_final: 0.8666 (mm110) REVERT: C 105 ARG cc_start: 0.9374 (tpp80) cc_final: 0.9032 (tpp80) REVERT: C 171 GLU cc_start: 0.8045 (mm-30) cc_final: 0.6968 (tm-30) REVERT: H 46 GLU cc_start: 0.8482 (tt0) cc_final: 0.7987 (tp30) REVERT: H 48 MET cc_start: 0.9306 (mtm) cc_final: 0.8296 (mtp) REVERT: H 98 MET cc_start: 0.7588 (ttt) cc_final: 0.6742 (tpt) REVERT: H 127 VAL cc_start: 0.7995 (t) cc_final: 0.7483 (m) REVERT: H 212 LYS cc_start: 0.9257 (tttm) cc_final: 0.8513 (mmtt) REVERT: H 215 LYS cc_start: 0.8390 (tppt) cc_final: 0.8131 (ttpt) REVERT: L 3 GLU cc_start: 0.8801 (tt0) cc_final: 0.8260 (tm-30) REVERT: L 4 LEU cc_start: 0.8768 (mt) cc_final: 0.8321 (tp) REVERT: L 84 ASP cc_start: 0.8915 (m-30) cc_final: 0.8688 (m-30) REVERT: L 86 TYR cc_start: 0.8463 (m-80) cc_final: 0.7996 (m-10) REVERT: L 99 TYR cc_start: 0.8568 (m-80) cc_final: 0.5903 (m-10) REVERT: L 136 LEU cc_start: 0.8792 (mt) cc_final: 0.8581 (mm) REVERT: L 143 PHE cc_start: 0.9024 (p90) cc_final: 0.8283 (p90) REVERT: L 182 LEU cc_start: 0.8813 (tt) cc_final: 0.8597 (tt) REVERT: L 184 LEU cc_start: 0.7995 (mt) cc_final: 0.7578 (tp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.2174 time to fit residues: 75.8453 Evaluate side-chains 175 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 54 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 0.0470 chunk 80 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- 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** B 30 HIS ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS L 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.066508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.051038 restraints weight = 49003.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.052912 restraints weight = 28170.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.054201 restraints weight = 18820.426| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5093 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= 0.181 Angle : 0.666 9.941 14930 Z= 0.338 Chirality : 0.044 0.239 1735 Planarity : 0.005 0.044 1862 Dihedral : 6.357 54.871 1745 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1336 helix: 0.89 (0.28), residues: 339 sheet: 0.71 (0.27), residues: 321 loop : -0.14 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 189 HIS 0.006 0.001 HIS A 528 PHE 0.018 0.002 PHE B 89 TYR 0.016 0.002 TYR C 117 ARG 0.003 0.000 ARG A 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 9) link_NAG-ASN : angle 3.00091 ( 27) link_ALPHA1-6 : bond 0.01162 ( 1) link_ALPHA1-6 : angle 1.08760 ( 3) link_BETA1-4 : bond 0.02208 ( 2) link_BETA1-4 : angle 3.73938 ( 6) link_ALPHA1-2 : bond 0.00512 ( 1) link_ALPHA1-2 : angle 1.96802 ( 3) link_ALPHA1-3 : bond 0.00548 ( 1) link_ALPHA1-3 : angle 2.38546 ( 3) hydrogen bonds : bond 0.04492 ( 483) hydrogen bonds : angle 5.52127 ( 1263) SS BOND : bond 0.00456 ( 16) SS BOND : angle 1.16756 ( 32) covalent geometry : bond 0.00387 (10909) covalent geometry : angle 0.64749 (14856) *********************** 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 221 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.9463 (tp) cc_final: 0.9260 (tp) REVERT: A 137 MET cc_start: 0.8360 (tmm) cc_final: 0.8121 (tmm) REVERT: A 138 LEU cc_start: 0.9100 (mt) cc_final: 0.8460 (mt) REVERT: A 160 LEU cc_start: 0.8864 (pt) cc_final: 0.8416 (tp) REVERT: A 217 THR cc_start: 0.9211 (m) cc_final: 0.8983 (t) REVERT: A 317 TRP cc_start: 0.9236 (t60) cc_final: 0.8731 (t60) REVERT: A 318 LEU cc_start: 0.9744 (mt) cc_final: 0.9420 (mt) REVERT: A 349 GLU cc_start: 0.9285 (tt0) cc_final: 0.8821 (tt0) REVERT: A 458 GLU cc_start: 0.8751 (tt0) cc_final: 0.7936 (tt0) REVERT: A 494 MET cc_start: 0.8476 (ttm) cc_final: 0.8251 (ttm) REVERT: A 543 MET cc_start: 0.7748 (tpp) cc_final: 0.7487 (tpp) REVERT: A 544 ILE cc_start: 0.9297 (mt) cc_final: 0.9061 (mt) REVERT: A 579 LEU cc_start: 0.9277 (tp) cc_final: 0.8338 (pp) REVERT: B 81 ASN cc_start: 0.8672 (t0) cc_final: 0.7965 (t0) REVERT: B 89 PHE cc_start: 0.9094 (m-80) cc_final: 0.8598 (m-80) REVERT: B 106 GLU cc_start: 0.9304 (tt0) cc_final: 0.8666 (tm-30) REVERT: B 107 LEU cc_start: 0.9504 (tp) cc_final: 0.9265 (tp) REVERT: C 73 ASP cc_start: 0.8303 (t0) cc_final: 0.8037 (t0) REVERT: C 81 TRP cc_start: 0.8698 (m-90) cc_final: 0.7739 (m100) REVERT: C 92 GLN cc_start: 0.8999 (mm110) cc_final: 0.8658 (mm110) REVERT: C 105 ARG cc_start: 0.9361 (tpp80) cc_final: 0.9082 (tpp80) REVERT: C 134 GLU cc_start: 0.8681 (pm20) cc_final: 0.8455 (pm20) REVERT: C 171 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7021 (tm-30) REVERT: H 46 GLU cc_start: 0.8594 (tt0) cc_final: 0.8024 (tp30) REVERT: H 48 MET cc_start: 0.9303 (mtm) cc_final: 0.8310 (mtp) REVERT: H 98 MET cc_start: 0.7759 (ttt) cc_final: 0.6872 (tpt) REVERT: H 160 TRP cc_start: 0.8399 (m100) cc_final: 0.8137 (m100) REVERT: H 212 LYS cc_start: 0.9204 (tttm) cc_final: 0.8518 (mmtt) REVERT: H 215 LYS cc_start: 0.8038 (tppt) cc_final: 0.7505 (tptp) REVERT: L 3 GLU cc_start: 0.8760 (tt0) cc_final: 0.8391 (tm-30) REVERT: L 4 LEU cc_start: 0.8779 (mt) cc_final: 0.8401 (tp) REVERT: L 49 TYR cc_start: 0.8235 (m-10) cc_final: 0.7918 (m-10) REVERT: L 84 ASP cc_start: 0.8815 (m-30) cc_final: 0.8607 (m-30) REVERT: L 86 TYR cc_start: 0.8458 (m-80) cc_final: 0.7883 (m-10) REVERT: L 99 TYR cc_start: 0.8633 (m-80) cc_final: 0.5867 (m-10) REVERT: L 136 LEU cc_start: 0.8728 (mt) cc_final: 0.8340 (mp) REVERT: L 140 ILE cc_start: 0.9430 (mp) cc_final: 0.9139 (mp) REVERT: L 143 PHE cc_start: 0.9008 (p90) cc_final: 0.8151 (p90) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1966 time to fit residues: 63.9363 Evaluate side-chains 172 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 92 optimal weight: 5.9990 chunk 104 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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** B 30 HIS C 103 ASN L 65 ASN L 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.052009 restraints weight = 48442.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.053914 restraints weight = 27704.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.055201 restraints weight = 18512.287| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10939 Z= 0.140 Angle : 0.651 10.033 14930 Z= 0.325 Chirality : 0.043 0.253 1735 Planarity : 0.005 0.043 1862 Dihedral : 6.140 59.435 1745 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.09 % Allowed : 1.29 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1336 helix: 0.99 (0.28), residues: 339 sheet: 0.75 (0.28), residues: 308 loop : -0.16 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 189 HIS 0.005 0.001 HIS A 426 PHE 0.030 0.002 PHE C 109 TYR 0.016 0.002 TYR C 101 ARG 0.004 0.000 ARG A 279 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 9) link_NAG-ASN : angle 3.76937 ( 27) link_ALPHA1-6 : bond 0.01151 ( 1) link_ALPHA1-6 : angle 1.14371 ( 3) link_BETA1-4 : bond 0.02055 ( 2) link_BETA1-4 : angle 3.59838 ( 6) link_ALPHA1-2 : bond 0.00619 ( 1) link_ALPHA1-2 : angle 1.85450 ( 3) link_ALPHA1-3 : bond 0.00757 ( 1) link_ALPHA1-3 : angle 2.35648 ( 3) hydrogen bonds : bond 0.04299 ( 483) hydrogen bonds : angle 5.39279 ( 1263) SS BOND : bond 0.00367 ( 16) SS BOND : angle 1.88748 ( 32) covalent geometry : bond 0.00303 (10909) covalent geometry : angle 0.62055 (14856) *********************** 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 219 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.8467 (tpp) cc_final: 0.8258 (mmm) REVERT: A 138 LEU cc_start: 0.9100 (mt) cc_final: 0.8478 (mt) REVERT: A 317 TRP cc_start: 0.9183 (t60) cc_final: 0.8718 (t60) REVERT: A 318 LEU cc_start: 0.9742 (mt) cc_final: 0.9477 (pp) REVERT: A 349 GLU cc_start: 0.9240 (tt0) cc_final: 0.8802 (tt0) REVERT: A 356 MET cc_start: 0.8373 (ppp) cc_final: 0.8142 (ppp) REVERT: A 451 THR cc_start: 0.9547 (m) cc_final: 0.9322 (p) REVERT: A 458 GLU cc_start: 0.8828 (tt0) cc_final: 0.8095 (tt0) REVERT: A 494 MET cc_start: 0.8414 (ttm) cc_final: 0.8181 (ttm) REVERT: A 544 ILE cc_start: 0.9291 (mt) cc_final: 0.9046 (mt) REVERT: A 579 LEU cc_start: 0.9263 (tp) cc_final: 0.8267 (pp) REVERT: B 81 ASN cc_start: 0.8461 (t0) cc_final: 0.7729 (t0) REVERT: B 100 LEU cc_start: 0.9149 (mt) cc_final: 0.8684 (mt) REVERT: B 106 GLU cc_start: 0.9314 (tt0) cc_final: 0.8785 (pt0) REVERT: C 73 ASP cc_start: 0.8254 (t0) cc_final: 0.7936 (t0) REVERT: C 81 TRP cc_start: 0.8696 (m-90) cc_final: 0.7864 (m100) REVERT: C 92 GLN cc_start: 0.9054 (mm110) cc_final: 0.8717 (mm110) REVERT: C 105 ARG cc_start: 0.9183 (tpp80) cc_final: 0.8928 (tpp80) REVERT: C 125 TRP cc_start: 0.7794 (t60) cc_final: 0.7150 (t60) REVERT: H 46 GLU cc_start: 0.8552 (tt0) cc_final: 0.8044 (tp30) REVERT: H 48 MET cc_start: 0.9313 (mtm) cc_final: 0.8329 (mtp) REVERT: H 98 MET cc_start: 0.7097 (ttt) cc_final: 0.6527 (tpt) REVERT: H 212 LYS cc_start: 0.9254 (tttm) cc_final: 0.8548 (mmtt) REVERT: H 215 LYS cc_start: 0.8117 (tppt) cc_final: 0.7671 (tptp) REVERT: L 3 GLU cc_start: 0.8773 (tt0) cc_final: 0.8393 (tm-30) REVERT: L 4 LEU cc_start: 0.8825 (mt) cc_final: 0.8399 (tp) REVERT: L 84 ASP cc_start: 0.8885 (m-30) cc_final: 0.8672 (m-30) REVERT: L 86 TYR cc_start: 0.8533 (m-80) cc_final: 0.8024 (m-10) REVERT: L 98 LEU cc_start: 0.8824 (pt) cc_final: 0.8462 (pt) REVERT: L 99 TYR cc_start: 0.8506 (m-80) cc_final: 0.5600 (m-10) REVERT: L 136 LEU cc_start: 0.8649 (mt) cc_final: 0.8270 (mp) REVERT: L 140 ILE cc_start: 0.9429 (mp) cc_final: 0.9102 (mp) REVERT: L 143 PHE cc_start: 0.9034 (p90) cc_final: 0.8231 (p90) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.1935 time to fit residues: 63.0848 Evaluate side-chains 168 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 86 optimal weight: 0.0770 chunk 90 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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** B 30 HIS H 205 ASN ** L 33 HIS ** 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 = 0.3173 r_free = 0.3173 target = 0.068377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.052963 restraints weight = 48423.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.054918 restraints weight = 27444.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.056252 restraints weight = 18230.202| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10939 Z= 0.125 Angle : 0.644 10.008 14930 Z= 0.322 Chirality : 0.044 0.272 1735 Planarity : 0.005 0.101 1862 Dihedral : 5.880 56.189 1745 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1336 helix: 0.97 (0.28), residues: 338 sheet: 0.72 (0.28), residues: 308 loop : -0.11 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP H 160 HIS 0.004 0.001 HIS A 426 PHE 0.025 0.002 PHE A 238 TYR 0.033 0.002 TYR L 49 ARG 0.009 0.000 ARG H 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 9) link_NAG-ASN : angle 3.18365 ( 27) link_ALPHA1-6 : bond 0.01078 ( 1) link_ALPHA1-6 : angle 1.16854 ( 3) link_BETA1-4 : bond 0.01979 ( 2) link_BETA1-4 : angle 3.58450 ( 6) link_ALPHA1-2 : bond 0.00707 ( 1) link_ALPHA1-2 : angle 1.64893 ( 3) link_ALPHA1-3 : bond 0.00886 ( 1) link_ALPHA1-3 : angle 2.34346 ( 3) hydrogen bonds : bond 0.04120 ( 483) hydrogen bonds : angle 5.26321 ( 1263) SS BOND : bond 0.00253 ( 16) SS BOND : angle 1.46233 ( 32) covalent geometry : bond 0.00271 (10909) covalent geometry : angle 0.62137 (14856) *********************** 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 : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.8469 (tpp) cc_final: 0.8229 (mmm) REVERT: A 138 LEU cc_start: 0.9061 (mt) cc_final: 0.8498 (mt) REVERT: A 160 LEU cc_start: 0.8762 (pt) cc_final: 0.8538 (pt) REVERT: A 291 MET cc_start: 0.9082 (ttm) cc_final: 0.8754 (ttp) REVERT: A 317 TRP cc_start: 0.9131 (t60) cc_final: 0.8705 (t60) REVERT: A 318 LEU cc_start: 0.9722 (mt) cc_final: 0.9465 (pp) REVERT: A 349 GLU cc_start: 0.9253 (tt0) cc_final: 0.8804 (tt0) REVERT: A 356 MET cc_start: 0.8379 (ppp) cc_final: 0.8145 (ppp) REVERT: A 451 THR cc_start: 0.9510 (m) cc_final: 0.9259 (p) REVERT: A 458 GLU cc_start: 0.8790 (tt0) cc_final: 0.7986 (tt0) REVERT: A 479 TYR cc_start: 0.9212 (m-10) cc_final: 0.9004 (m-80) REVERT: A 544 ILE cc_start: 0.9297 (mt) cc_final: 0.9038 (mt) REVERT: A 579 LEU cc_start: 0.9256 (tp) cc_final: 0.8302 (pp) REVERT: A 640 GLN cc_start: 0.9051 (tt0) cc_final: 0.8342 (mt0) REVERT: B 81 ASN cc_start: 0.8623 (t0) cc_final: 0.8266 (t0) REVERT: B 89 PHE cc_start: 0.9029 (m-80) cc_final: 0.8309 (m-80) REVERT: B 93 LEU cc_start: 0.9568 (mt) cc_final: 0.9366 (mt) REVERT: B 100 LEU cc_start: 0.9153 (mt) cc_final: 0.8660 (mt) REVERT: B 106 GLU cc_start: 0.9300 (tt0) cc_final: 0.8770 (pt0) REVERT: C 73 ASP cc_start: 0.8189 (t0) cc_final: 0.7888 (t0) REVERT: C 81 TRP cc_start: 0.8626 (m-90) cc_final: 0.7758 (m100) REVERT: C 92 GLN cc_start: 0.9063 (mm110) cc_final: 0.8729 (mm110) REVERT: C 125 TRP cc_start: 0.7878 (t60) cc_final: 0.7144 (t60) REVERT: C 171 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7076 (tm-30) REVERT: H 46 GLU cc_start: 0.8542 (tt0) cc_final: 0.8164 (tp30) REVERT: H 48 MET cc_start: 0.9306 (mtm) cc_final: 0.8445 (mtp) REVERT: H 69 MET cc_start: 0.7476 (mmp) cc_final: 0.7273 (mmm) REVERT: H 98 MET cc_start: 0.6955 (ttt) cc_final: 0.6449 (tpt) REVERT: H 127 VAL cc_start: 0.7972 (t) cc_final: 0.7314 (m) REVERT: H 212 LYS cc_start: 0.9257 (tttm) cc_final: 0.8464 (mmtt) REVERT: L 3 GLU cc_start: 0.8747 (tt0) cc_final: 0.8219 (tm-30) REVERT: L 4 LEU cc_start: 0.8730 (mt) cc_final: 0.8063 (tt) REVERT: L 31 ASN cc_start: 0.9056 (m-40) cc_final: 0.8665 (m-40) REVERT: L 36 GLN cc_start: 0.8655 (pp30) cc_final: 0.8359 (pm20) REVERT: L 84 ASP cc_start: 0.8865 (m-30) cc_final: 0.8647 (m-30) REVERT: L 86 TYR cc_start: 0.8534 (m-80) cc_final: 0.8024 (m-10) REVERT: L 99 TYR cc_start: 0.8438 (m-80) cc_final: 0.5626 (m-10) REVERT: L 140 ILE cc_start: 0.9408 (mp) cc_final: 0.9075 (mp) REVERT: L 143 PHE cc_start: 0.9029 (p90) cc_final: 0.8228 (p90) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1994 time to fit residues: 64.2620 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 : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 85 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.0770 chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.7944 ------------------------------------------------------------------------------- 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** B 30 HIS L 33 HIS L 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.068649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.053310 restraints weight = 48017.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.055262 restraints weight = 27300.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.056617 restraints weight = 18111.660| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10939 Z= 0.123 Angle : 0.627 9.997 14930 Z= 0.312 Chirality : 0.044 0.278 1735 Planarity : 0.005 0.046 1862 Dihedral : 5.738 55.383 1745 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.23), residues: 1336 helix: 0.99 (0.28), residues: 336 sheet: 0.77 (0.28), residues: 315 loop : -0.11 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 189 HIS 0.005 0.001 HIS A 426 PHE 0.019 0.002 PHE A 298 TYR 0.024 0.002 TYR L 49 ARG 0.007 0.000 ARG H 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 9) link_NAG-ASN : angle 2.99304 ( 27) link_ALPHA1-6 : bond 0.01081 ( 1) link_ALPHA1-6 : angle 1.13801 ( 3) link_BETA1-4 : bond 0.01987 ( 2) link_BETA1-4 : angle 3.53056 ( 6) link_ALPHA1-2 : bond 0.00702 ( 1) link_ALPHA1-2 : angle 1.63652 ( 3) link_ALPHA1-3 : bond 0.00876 ( 1) link_ALPHA1-3 : angle 2.39842 ( 3) hydrogen bonds : bond 0.03982 ( 483) hydrogen bonds : angle 5.22182 ( 1263) SS BOND : bond 0.00246 ( 16) SS BOND : angle 1.23506 ( 32) covalent geometry : bond 0.00272 (10909) covalent geometry : angle 0.60736 (14856) ********************** 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 214 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.8539 (tpp) cc_final: 0.8278 (mmm) REVERT: A 138 LEU cc_start: 0.9063 (mt) cc_final: 0.8544 (mt) REVERT: A 151 LEU cc_start: 0.8843 (tp) cc_final: 0.8544 (tp) REVERT: A 163 ASN cc_start: 0.8340 (m-40) cc_final: 0.8068 (m-40) REVERT: A 291 MET cc_start: 0.9058 (ttm) cc_final: 0.8738 (ttp) REVERT: A 317 TRP cc_start: 0.9102 (t60) cc_final: 0.8662 (t60) REVERT: A 318 LEU cc_start: 0.9744 (mt) cc_final: 0.9482 (pp) REVERT: A 349 GLU cc_start: 0.9277 (tt0) cc_final: 0.8856 (tt0) REVERT: A 356 MET cc_start: 0.8350 (ppp) cc_final: 0.8122 (ppp) REVERT: A 451 THR cc_start: 0.9538 (m) cc_final: 0.9281 (p) REVERT: A 458 GLU cc_start: 0.8775 (tt0) cc_final: 0.8042 (tt0) REVERT: A 544 ILE cc_start: 0.9326 (mt) cc_final: 0.9074 (mt) REVERT: A 579 LEU cc_start: 0.9300 (tp) cc_final: 0.8305 (pp) REVERT: A 614 PHE cc_start: 0.8910 (m-10) cc_final: 0.8575 (m-10) REVERT: A 640 GLN cc_start: 0.9030 (tt0) cc_final: 0.8370 (mt0) REVERT: B 47 ASP cc_start: 0.9095 (m-30) cc_final: 0.8870 (m-30) REVERT: B 81 ASN cc_start: 0.8694 (t0) cc_final: 0.8398 (t0) REVERT: B 89 PHE cc_start: 0.9035 (m-80) cc_final: 0.8343 (m-80) REVERT: B 106 GLU cc_start: 0.9292 (tt0) cc_final: 0.8764 (pt0) REVERT: C 73 ASP cc_start: 0.8208 (t0) cc_final: 0.7899 (t0) REVERT: C 81 TRP cc_start: 0.8595 (m-90) cc_final: 0.8022 (m100) REVERT: C 92 GLN cc_start: 0.9061 (mm110) cc_final: 0.8733 (mm110) REVERT: C 125 TRP cc_start: 0.7822 (t60) cc_final: 0.7239 (t60) REVERT: C 171 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7058 (tm-30) REVERT: H 46 GLU cc_start: 0.8552 (tt0) cc_final: 0.8221 (tp30) REVERT: H 48 MET cc_start: 0.9314 (mtm) cc_final: 0.8450 (mtp) REVERT: H 69 MET cc_start: 0.7498 (mmp) cc_final: 0.6766 (mmm) REVERT: H 98 MET cc_start: 0.7130 (ttt) cc_final: 0.6480 (tpt) REVERT: H 212 LYS cc_start: 0.9251 (tttm) cc_final: 0.8462 (mmtt) REVERT: L 3 GLU cc_start: 0.8738 (tt0) cc_final: 0.8192 (tm-30) REVERT: L 4 LEU cc_start: 0.8764 (mt) cc_final: 0.8093 (tt) REVERT: L 31 ASN cc_start: 0.9004 (m-40) cc_final: 0.7464 (t0) REVERT: L 86 TYR cc_start: 0.8500 (m-80) cc_final: 0.8008 (m-10) REVERT: L 98 LEU cc_start: 0.8781 (pt) cc_final: 0.8407 (pt) REVERT: L 99 TYR cc_start: 0.8460 (m-80) cc_final: 0.5790 (m-10) REVERT: L 140 ILE cc_start: 0.9416 (mp) cc_final: 0.9095 (mp) REVERT: L 143 PHE cc_start: 0.9031 (p90) cc_final: 0.8241 (p90) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1805 time to fit residues: 58.7055 Evaluate side-chains 172 residues out of total 1162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 26 optimal weight: 0.0980 chunk 98 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 655 HIS A 657 HIS B 30 HIS C 92 GLN ** H 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.066864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.051718 restraints weight = 48386.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.053603 restraints weight = 27723.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.054852 restraints weight = 18457.256| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10939 Z= 0.173 Angle : 0.667 9.767 14930 Z= 0.336 Chirality : 0.044 0.275 1735 Planarity : 0.005 0.045 1862 Dihedral : 5.841 55.472 1745 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1336 helix: 0.85 (0.28), residues: 336 sheet: 0.64 (0.28), residues: 310 loop : -0.25 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 189 HIS 0.004 0.001 HIS A 528 PHE 0.031 0.002 PHE B 88 TYR 0.024 0.002 TYR H 108 ARG 0.006 0.001 ARG H 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 9) link_NAG-ASN : angle 3.00808 ( 27) link_ALPHA1-6 : bond 0.01303 ( 1) link_ALPHA1-6 : angle 0.96185 ( 3) link_BETA1-4 : bond 0.01981 ( 2) link_BETA1-4 : angle 3.67292 ( 6) link_ALPHA1-2 : bond 0.00587 ( 1) link_ALPHA1-2 : angle 1.97374 ( 3) link_ALPHA1-3 : bond 0.00679 ( 1) link_ALPHA1-3 : angle 2.50508 ( 3) hydrogen bonds : bond 0.04301 ( 483) hydrogen bonds : angle 5.40273 ( 1263) SS BOND : bond 0.00294 ( 16) SS BOND : angle 1.22033 ( 32) covalent geometry : bond 0.00376 (10909) covalent geometry : angle 0.64752 (14856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3808.58 seconds wall clock time: 68 minutes 41.91 seconds (4121.91 seconds total)