Starting phenix.real_space_refine on Fri Sep 11 07:16:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xi9_66901/09_2026/9xi9_66901.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xi9_66901/09_2026/9xi9_66901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xi9_66901/09_2026/9xi9_66901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xi9_66901/09_2026/9xi9_66901.map" model { file = "/net/cci-nas-00/data/ceres_data/9xi9_66901/09_2026/9xi9_66901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xi9_66901/09_2026/9xi9_66901.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.036 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 33 5.16 5 C 5097 2.51 5 N 1349 2.21 5 O 1607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8086 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1645 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "B" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1610 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 200} Chain: "H" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1584 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "C" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1559 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain: "L" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1649 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: 1.86, per 1000 atoms: 0.23 Number of scatterers: 8086 At special positions: 0 Unit cell: (166.116, 66.4462, 115.243, 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 33 16.00 O 1607 8.00 N 1349 7.00 C 5097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG D 1 " - " ASN C 354 " Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 389.0 milliseconds 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 27 sheets defined 9.7% alpha, 46.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.739A pdb=" N THR A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.516A pdb=" N ASP B 84 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU B 85 " --> pdb=" O ALA B 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 81 through 85' Processing helix chain 'B' and resid 126 through 132 Processing helix chain 'B' and resid 186 through 193 removed outlier: 3.653A pdb=" N HIS B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 34 removed outlier: 3.804A pdb=" N ASN H 34 " --> pdb=" O VAL H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' 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 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.033A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.148A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.938A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 removed outlier: 3.587A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.559A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.620A pdb=" N MET A 18 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 83 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.549A pdb=" N ILE A 34 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.652A pdb=" N CYS A 96 " --> pdb=" O TRP A 114 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TRP A 114 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS A 98 " --> pdb=" O HIS A 112 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A 110 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 135 removed outlier: 4.321A pdb=" N GLY A 150 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR A 187 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 134 through 135 removed outlier: 4.321A pdb=" N GLY A 150 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR A 187 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 162 through 165 removed outlier: 4.224A pdb=" N TYR A 205 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.772A pdb=" N VAL B 10 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TRP B 37 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.772A pdb=" N VAL B 10 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AB2, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.773A pdb=" N VAL B 138 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR B 177 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.773A pdb=" N VAL B 138 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR B 177 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 158 through 160 removed outlier: 3.632A pdb=" N TRP B 153 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 209 " --> pdb=" O CYS B 198 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 7 through 8 Processing sheet with id=AB6, first strand: chain 'H' and resid 13 through 14 removed outlier: 3.805A pdb=" N TYR H 35 " --> pdb=" O GLN H 100 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET H 36 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE H 52 " --> pdb=" O MET H 36 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP H 38 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 13 through 14 removed outlier: 4.034A pdb=" N PHE H 108 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.870A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP H 150 " --> pdb=" O TYR H 182 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 137 through 138 removed outlier: 3.623A pdb=" N ASP H 150 " --> pdb=" O TYR H 182 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER H 183 " --> pdb=" O VAL H 175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 157 through 160 removed outlier: 4.481A pdb=" N TYR H 200 " --> pdb=" O VAL H 217 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.613A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.618A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.618A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.827A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN L 138 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR L 178 " --> pdb=" O GLN L 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.461A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2574 1.34 - 1.46: 2029 1.46 - 1.58: 3646 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 8289 Sorted by residual: bond pdb=" C GLU A 159 " pdb=" N PRO A 160 " ideal model delta sigma weight residual 1.333 1.346 -0.013 7.80e-03 1.64e+04 2.61e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.543 -0.024 2.00e-02 2.50e+03 1.39e+00 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.433 -0.020 2.00e-02 2.50e+03 1.00e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.426 -0.020 2.00e-02 2.50e+03 9.71e-01 ... (remaining 8284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 10922 1.22 - 2.44: 261 2.44 - 3.66: 77 3.66 - 4.87: 19 4.87 - 6.09: 10 Bond angle restraints: 11289 Sorted by residual: angle pdb=" C PRO A 158 " pdb=" N GLU A 159 " pdb=" CA GLU A 159 " ideal model delta sigma weight residual 122.28 118.29 3.99 1.02e+00 9.61e-01 1.53e+01 angle pdb=" N ILE B 29 " pdb=" CA ILE B 29 " pdb=" C ILE B 29 " ideal model delta sigma weight residual 112.96 109.20 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" C ARG B 52 " pdb=" N ASN B 53 " pdb=" CA ASN B 53 " ideal model delta sigma weight residual 121.54 127.39 -5.85 1.91e+00 2.74e-01 9.37e+00 angle pdb=" CA VAL A 195 " pdb=" C VAL A 195 " pdb=" N PRO A 196 " ideal model delta sigma weight residual 116.57 119.02 -2.45 9.80e-01 1.04e+00 6.24e+00 angle pdb=" C ASP A 73 " pdb=" N THR A 74 " pdb=" CA THR A 74 " ideal model delta sigma weight residual 121.54 125.42 -3.88 1.91e+00 2.74e-01 4.13e+00 ... (remaining 11284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.42: 4711 21.42 - 42.84: 225 42.84 - 64.27: 21 64.27 - 85.69: 16 85.69 - 107.11: 4 Dihedral angle restraints: 4977 sinusoidal: 1925 harmonic: 3052 Sorted by residual: dihedral pdb=" SG CYS C 391 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " pdb=" CA CYS C 525 " ideal model delta sinusoidal sigma weight residual -73.00 -2.74 -70.26 1 2.00e+01 2.50e-03 1.59e+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 -178.40 107.11 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C3 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 47.62 -57.61 105.23 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 4974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1067 0.055 - 0.110: 163 0.110 - 0.165: 32 0.165 - 0.220: 0 0.220 - 0.275: 1 Chirality restraints: 1263 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN C 354 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA ILE B 141 " pdb=" N ILE B 141 " pdb=" C ILE B 141 " pdb=" CB ILE B 141 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 1260 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 373 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 13 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO A 14 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 14 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 14 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.99e+00 pdb=" N PRO C 527 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " 0.019 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 593 2.74 - 3.28: 7522 3.28 - 3.82: 13662 3.82 - 4.36: 16721 4.36 - 4.90: 29055 Nonbonded interactions: 67553 Sorted by model distance: nonbonded pdb=" OG SER C 438 " pdb=" OD2 ASP C 442 " model vdw 2.204 3.040 nonbonded pdb=" OE1 GLU C 406 " pdb=" OH TYR C 495 " model vdw 2.234 3.040 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.292 3.040 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.305 3.040 nonbonded pdb=" O ASP B 84 " pdb=" OH TYR B 88 " model vdw 2.333 3.040 ... (remaining 67548 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 individual isotropic 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.510 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 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 : 0.003 0.030 8304 Z= 0.127 Angle : 0.546 8.514 11322 Z= 0.276 Chirality : 0.044 0.275 1263 Planarity : 0.004 0.038 1451 Dihedral : 13.033 107.112 2999 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.27), residues: 1051 helix: -2.12 (0.64), residues: 51 sheet: 0.65 (0.26), residues: 433 loop : 0.25 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 68 TYR 0.024 0.001 TYR B 177 PHE 0.015 0.001 PHE C 377 TRP 0.008 0.001 TRP A 36 HIS 0.001 0.000 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 8289) covalent geometry : angle 0.53600 / 0.27 (11289) SS BOND : bond 0.00185 / 0.13 ( 12) SS BOND : angle 0.59207 / 0.39 ( 24) hydrogen bonds : bond 0.25752 / 17.77 ( 294) hydrogen bonds : angle 10.62322 / 7.40 ( 822) link_BETA1-4 : bond 0.00244 / 0.12 ( 2) link_BETA1-4 : angle 1.31538 / 0.63 ( 6) link_NAG-ASN : bond 0.00666 / 0.35 ( 1) link_NAG-ASN : angle 6.14942 / 3.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.308 Fit side-chains REVERT: A 10 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7605 (mt-10) REVERT: B 177 TYR cc_start: 0.6177 (m-10) cc_final: 0.5960 (m-10) REVERT: C 386 LYS cc_start: 0.7724 (mmpt) cc_final: 0.7018 (ttpp) REVERT: C 478 LYS cc_start: 0.8414 (mttt) cc_final: 0.8076 (mttm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.5892 time to fit residues: 65.7763 Evaluate side-chains 81 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 8 GLN C 394 ASN C 417 ASN L 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.193057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126723 restraints weight = 8845.368| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.94 r_work: 0.3032 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 8304 Z= 0.308 Angle : 0.701 8.788 11322 Z= 0.360 Chirality : 0.049 0.175 1263 Planarity : 0.005 0.043 1451 Dihedral : 6.354 54.058 1203 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.55 % Allowed : 7.33 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1051 helix: -2.35 (0.57), residues: 54 sheet: 0.49 (0.25), residues: 440 loop : -0.07 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 105 TYR 0.026 0.002 TYR B 177 PHE 0.017 0.002 PHE L 71 TRP 0.019 0.003 TRP A 36 HIS 0.005 0.001 HIS L 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.31 ( 8289) covalent geometry : angle 0.69206 / 0.36 (11289) SS BOND : bond 0.00531 / 0.38 ( 12) SS BOND : angle 1.31342 / 0.88 ( 24) hydrogen bonds : bond 0.04559 / 3.02 ( 294) hydrogen bonds : angle 7.04929 / 4.96 ( 822) link_BETA1-4 : bond 0.00641 / 0.34 ( 2) link_BETA1-4 : angle 3.04669 / 1.56 ( 6) link_NAG-ASN : bond 0.00905 / 0.48 ( 1) link_NAG-ASN : angle 4.66832 / 2.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.278 Fit side-chains REVERT: A 128 LYS cc_start: 0.7254 (mtmt) cc_final: 0.6515 (ttmm) REVERT: B 1 GLN cc_start: 0.7714 (pm20) cc_final: 0.7270 (pm20) REVERT: B 165 GLU cc_start: 0.6764 (mp0) cc_final: 0.6042 (mm-30) REVERT: H 66 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7517 (ttmt) REVERT: H 77 LYS cc_start: 0.7035 (mtpp) cc_final: 0.6746 (mtpp) REVERT: C 386 LYS cc_start: 0.7889 (mmpt) cc_final: 0.6756 (tmmt) REVERT: C 478 LYS cc_start: 0.8406 (mttt) cc_final: 0.7876 (mttm) REVERT: L 32 TYR cc_start: 0.9100 (m-80) cc_final: 0.8888 (m-80) REVERT: L 106 LEU cc_start: 0.7791 (tp) cc_final: 0.7542 (tp) outliers start: 14 outliers final: 8 residues processed: 90 average time/residue: 0.5206 time to fit residues: 49.7566 Evaluate side-chains 87 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain L residue 14 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 41 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN L 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.194931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128060 restraints weight = 8835.900| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.37 r_work: 0.3041 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8304 Z= 0.179 Angle : 0.594 7.048 11322 Z= 0.301 Chirality : 0.045 0.168 1263 Planarity : 0.004 0.047 1451 Dihedral : 5.260 34.131 1203 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.44 % Allowed : 9.21 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.26), residues: 1051 helix: -2.26 (0.58), residues: 54 sheet: 0.58 (0.25), residues: 440 loop : 0.02 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.017 0.002 TYR B 177 PHE 0.012 0.002 PHE A 111 TRP 0.011 0.002 TRP A 36 HIS 0.003 0.001 HIS L 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 8289) covalent geometry : angle 0.58636 / 0.30 (11289) SS BOND : bond 0.00385 / 0.27 ( 12) SS BOND : angle 0.83639 / 0.58 ( 24) hydrogen bonds : bond 0.03675 / 2.42 ( 294) hydrogen bonds : angle 6.24359 / 4.41 ( 822) link_BETA1-4 : bond 0.00339 / 0.16 ( 2) link_BETA1-4 : angle 2.66786 / 1.37 ( 6) link_NAG-ASN : bond 0.00570 / 0.30 ( 1) link_NAG-ASN : angle 4.06441 / 2.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.284 Fit side-chains REVERT: A 48 MET cc_start: 0.9284 (mtm) cc_final: 0.9063 (mtp) REVERT: B 165 GLU cc_start: 0.6931 (mp0) cc_final: 0.5971 (mm-30) REVERT: H 33 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.8282 (mtm-85) REVERT: H 37 ASN cc_start: 0.9076 (m110) cc_final: 0.8844 (m-40) REVERT: H 66 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7536 (ttmt) REVERT: H 77 LYS cc_start: 0.7010 (mtpp) cc_final: 0.6724 (mtpp) REVERT: H 111 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: C 386 LYS cc_start: 0.7918 (mmpt) cc_final: 0.6768 (tmmt) REVERT: C 478 LYS cc_start: 0.8475 (mttt) cc_final: 0.7944 (mttm) REVERT: L 70 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: L 106 LEU cc_start: 0.7782 (tp) cc_final: 0.7539 (tp) outliers start: 13 outliers final: 6 residues processed: 92 average time/residue: 0.5554 time to fit residues: 54.1442 Evaluate side-chains 92 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 70 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 94 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN H 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.195320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.146852 restraints weight = 9101.235| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.56 r_work: 0.3170 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8304 Z= 0.141 Angle : 0.562 8.160 11322 Z= 0.284 Chirality : 0.044 0.152 1263 Planarity : 0.004 0.046 1451 Dihedral : 4.666 22.588 1203 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.55 % Allowed : 10.54 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 1051 helix: -2.15 (0.59), residues: 54 sheet: 0.67 (0.25), residues: 433 loop : 0.05 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.012 0.001 TYR B 177 PHE 0.011 0.001 PHE A 111 TRP 0.010 0.001 TRP A 36 HIS 0.003 0.001 HIS L 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8289) covalent geometry : angle 0.55533 / 0.28 (11289) SS BOND : bond 0.00277 / 0.19 ( 12) SS BOND : angle 0.68953 / 0.46 ( 24) hydrogen bonds : bond 0.03093 / 2.04 ( 294) hydrogen bonds : angle 5.76035 / 4.08 ( 822) link_BETA1-4 : bond 0.00260 / 0.12 ( 2) link_BETA1-4 : angle 2.32828 / 1.18 ( 6) link_NAG-ASN : bond 0.00456 / 0.24 ( 1) link_NAG-ASN : angle 3.96347 / 2.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.324 Fit side-chains REVERT: A 84 ARG cc_start: 0.9141 (mtm-85) cc_final: 0.8882 (mpp-170) REVERT: A 128 LYS cc_start: 0.7497 (mtmt) cc_final: 0.6684 (ttmm) REVERT: B 165 GLU cc_start: 0.7264 (mp0) cc_final: 0.6382 (mm-30) REVERT: H 33 ARG cc_start: 0.8600 (mtm-85) cc_final: 0.8365 (mtm-85) REVERT: H 66 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7626 (ttmt) REVERT: H 111 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7579 (pm20) REVERT: C 386 LYS cc_start: 0.7980 (mmpt) cc_final: 0.7108 (tmmt) REVERT: C 478 LYS cc_start: 0.8598 (mttt) cc_final: 0.8152 (mttm) REVERT: L 24 GLN cc_start: 0.8146 (pt0) cc_final: 0.7662 (mt0) REVERT: L 70 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: L 106 LEU cc_start: 0.8009 (tp) cc_final: 0.7786 (tp) outliers start: 14 outliers final: 10 residues processed: 92 average time/residue: 0.5598 time to fit residues: 54.6384 Evaluate side-chains 95 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.195507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.146874 restraints weight = 8936.935| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.55 r_work: 0.3168 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8304 Z= 0.146 Angle : 0.559 7.603 11322 Z= 0.283 Chirality : 0.044 0.151 1263 Planarity : 0.004 0.046 1451 Dihedral : 4.502 19.267 1203 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.55 % Allowed : 11.99 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.26), residues: 1051 helix: -2.06 (0.61), residues: 54 sheet: 0.72 (0.25), residues: 432 loop : 0.03 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 18 TYR 0.012 0.001 TYR H 151 PHE 0.011 0.001 PHE A 111 TRP 0.011 0.001 TRP A 36 HIS 0.003 0.001 HIS L 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 8289) covalent geometry : angle 0.55303 / 0.28 (11289) SS BOND : bond 0.00294 / 0.21 ( 12) SS BOND : angle 0.71477 / 0.48 ( 24) hydrogen bonds : bond 0.02987 / 1.96 ( 294) hydrogen bonds : angle 5.53448 / 3.91 ( 822) link_BETA1-4 : bond 0.00274 / 0.13 ( 2) link_BETA1-4 : angle 2.00666 / 1.03 ( 6) link_NAG-ASN : bond 0.00498 / 0.26 ( 1) link_NAG-ASN : angle 4.05511 / 2.31 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.270 Fit side-chains REVERT: A 84 ARG cc_start: 0.9128 (mtm-85) cc_final: 0.8812 (mpp-170) REVERT: A 128 LYS cc_start: 0.7519 (mtmt) cc_final: 0.6931 (ttmm) REVERT: B 165 GLU cc_start: 0.7275 (mp0) cc_final: 0.6382 (mm-30) REVERT: H 33 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8357 (mtm-85) REVERT: H 37 ASN cc_start: 0.8884 (m-40) cc_final: 0.8660 (m-40) REVERT: H 66 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7619 (ttmt) REVERT: H 77 LYS cc_start: 0.7605 (mtpp) cc_final: 0.7367 (ptpt) REVERT: H 111 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: C 386 LYS cc_start: 0.7977 (mmpt) cc_final: 0.7097 (tmmt) REVERT: L 24 GLN cc_start: 0.8111 (pt0) cc_final: 0.7673 (mt0) REVERT: L 70 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: L 106 LEU cc_start: 0.7997 (tp) cc_final: 0.7772 (tp) outliers start: 14 outliers final: 10 residues processed: 91 average time/residue: 0.5476 time to fit residues: 52.9630 Evaluate side-chains 96 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 54 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN H 106 ASN L 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.193716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.145691 restraints weight = 8965.473| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.51 r_work: 0.3133 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8304 Z= 0.219 Angle : 0.607 8.283 11322 Z= 0.307 Chirality : 0.046 0.157 1263 Planarity : 0.004 0.045 1451 Dihedral : 4.754 19.837 1203 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.22 % Allowed : 12.43 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.26), residues: 1051 helix: -2.08 (0.60), residues: 54 sheet: 0.44 (0.24), residues: 456 loop : 0.03 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 18 TYR 0.019 0.002 TYR H 151 PHE 0.012 0.002 PHE H 69 TRP 0.014 0.002 TRP A 36 HIS 0.004 0.001 HIS L 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 ( 8289) covalent geometry : angle 0.60013 / 0.30 (11289) SS BOND : bond 0.00423 / 0.30 ( 12) SS BOND : angle 0.90377 / 0.60 ( 24) hydrogen bonds : bond 0.03290 / 2.16 ( 294) hydrogen bonds : angle 5.69062 / 4.01 ( 822) link_BETA1-4 : bond 0.00404 / 0.21 ( 2) link_BETA1-4 : angle 2.09344 / 1.09 ( 6) link_NAG-ASN : bond 0.00787 / 0.41 ( 1) link_NAG-ASN : angle 4.34312 / 2.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.313 Fit side-chains REVERT: A 84 ARG cc_start: 0.9120 (mtm-85) cc_final: 0.8831 (mpp-170) REVERT: A 89 GLN cc_start: 0.8308 (pp30) cc_final: 0.7993 (pm20) REVERT: B 122 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6503 (tp) REVERT: B 165 GLU cc_start: 0.7289 (mp0) cc_final: 0.6375 (mm-30) REVERT: H 37 ASN cc_start: 0.8907 (m110) cc_final: 0.8698 (m-40) REVERT: H 66 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7641 (ttmt) REVERT: H 77 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7408 (ptpt) REVERT: H 111 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7856 (pm20) REVERT: C 386 LYS cc_start: 0.8050 (mmpt) cc_final: 0.7130 (tmmt) REVERT: C 478 LYS cc_start: 0.8514 (mttt) cc_final: 0.8127 (mttm) REVERT: L 24 GLN cc_start: 0.8111 (pt0) cc_final: 0.7656 (mt0) REVERT: L 70 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7675 (mp0) outliers start: 20 outliers final: 12 residues processed: 96 average time/residue: 0.5049 time to fit residues: 51.7440 Evaluate side-chains 99 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain H residue 21 ARG Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 39 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 64 optimal weight: 0.0770 chunk 16 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN H 37 ASN H 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.196163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.142947 restraints weight = 8982.255| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.62 r_work: 0.3166 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8304 Z= 0.121 Angle : 0.546 7.603 11322 Z= 0.276 Chirality : 0.043 0.154 1263 Planarity : 0.004 0.048 1451 Dihedral : 4.455 19.636 1203 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.78 % Allowed : 13.65 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1051 helix: -1.96 (0.61), residues: 54 sheet: 0.81 (0.25), residues: 432 loop : 0.02 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.013 0.001 TYR B 177 PHE 0.011 0.001 PHE A 111 TRP 0.009 0.001 TRP A 36 HIS 0.002 0.000 HIS L 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 8289) covalent geometry : angle 0.54084 / 0.27 (11289) SS BOND : bond 0.00260 / 0.18 ( 12) SS BOND : angle 0.64045 / 0.42 ( 24) hydrogen bonds : bond 0.02758 / 1.81 ( 294) hydrogen bonds : angle 5.34898 / 3.78 ( 822) link_BETA1-4 : bond 0.00224 / 0.11 ( 2) link_BETA1-4 : angle 1.78107 / 0.91 ( 6) link_NAG-ASN : bond 0.00366 / 0.19 ( 1) link_NAG-ASN : angle 3.78119 / 2.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.310 Fit side-chains REVERT: A 84 ARG cc_start: 0.9123 (mtm-85) cc_final: 0.8839 (mpp-170) REVERT: A 89 GLN cc_start: 0.8330 (pp30) cc_final: 0.8023 (pm20) REVERT: B 122 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6473 (tp) REVERT: B 165 GLU cc_start: 0.7256 (mp0) cc_final: 0.6341 (mm-30) REVERT: H 33 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8371 (mtm-85) REVERT: H 66 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7620 (ttmt) REVERT: H 77 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7421 (ptpt) REVERT: H 111 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: C 386 LYS cc_start: 0.8033 (mmpt) cc_final: 0.7103 (tmmt) REVERT: L 24 GLN cc_start: 0.8095 (pt0) cc_final: 0.7679 (mt0) REVERT: L 70 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7661 (mp0) outliers start: 16 outliers final: 9 residues processed: 89 average time/residue: 0.5215 time to fit residues: 49.5064 Evaluate side-chains 94 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 83 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 73 optimal weight: 0.0870 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN H 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.195676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.142546 restraints weight = 8911.680| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.68 r_work: 0.3133 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8304 Z= 0.143 Angle : 0.559 8.377 11322 Z= 0.281 Chirality : 0.044 0.151 1263 Planarity : 0.004 0.045 1451 Dihedral : 4.455 19.357 1203 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.89 % Allowed : 14.10 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1051 helix: -1.94 (0.61), residues: 54 sheet: 0.81 (0.24), residues: 432 loop : 0.02 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.014 0.001 TYR B 177 PHE 0.011 0.001 PHE A 111 TRP 0.010 0.001 TRP A 36 HIS 0.003 0.001 HIS L 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 8289) covalent geometry : angle 0.55319 / 0.28 (11289) SS BOND : bond 0.00287 / 0.20 ( 12) SS BOND : angle 0.70628 / 0.47 ( 24) hydrogen bonds : bond 0.02824 / 1.86 ( 294) hydrogen bonds : angle 5.32760 / 3.76 ( 822) link_BETA1-4 : bond 0.00269 / 0.13 ( 2) link_BETA1-4 : angle 1.81544 / 0.93 ( 6) link_NAG-ASN : bond 0.00515 / 0.27 ( 1) link_NAG-ASN : angle 4.09129 / 2.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.300 Fit side-chains REVERT: A 84 ARG cc_start: 0.9107 (mtm-85) cc_final: 0.8804 (mpp-170) REVERT: A 89 GLN cc_start: 0.8352 (pp30) cc_final: 0.8017 (pm20) REVERT: B 122 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6499 (tp) REVERT: B 165 GLU cc_start: 0.7275 (mp0) cc_final: 0.6358 (mm-30) REVERT: H 33 ARG cc_start: 0.8665 (mtm-85) cc_final: 0.8409 (mtm-85) REVERT: H 66 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7669 (ttmt) REVERT: H 77 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7449 (ptpt) REVERT: H 111 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: C 386 LYS cc_start: 0.8047 (mmpt) cc_final: 0.7116 (tmmt) REVERT: L 24 GLN cc_start: 0.8088 (pt0) cc_final: 0.7682 (mt0) REVERT: L 70 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7670 (mp0) outliers start: 17 outliers final: 10 residues processed: 93 average time/residue: 0.5340 time to fit residues: 52.7412 Evaluate side-chains 93 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 81 optimal weight: 0.5980 chunk 76 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.196575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.143198 restraints weight = 8886.376| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.55 r_work: 0.3180 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8304 Z= 0.118 Angle : 0.549 7.970 11322 Z= 0.275 Chirality : 0.043 0.152 1263 Planarity : 0.004 0.047 1451 Dihedral : 4.355 18.986 1203 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.66 % Allowed : 14.43 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.26), residues: 1051 helix: -1.87 (0.62), residues: 55 sheet: 0.88 (0.25), residues: 432 loop : 0.07 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.016 0.001 TYR B 177 PHE 0.010 0.001 PHE A 111 TRP 0.008 0.001 TRP A 36 HIS 0.002 0.000 HIS L 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 8289) covalent geometry : angle 0.54397 / 0.27 (11289) SS BOND : bond 0.00227 / 0.15 ( 12) SS BOND : angle 0.68855 / 0.46 ( 24) hydrogen bonds : bond 0.02653 / 1.76 ( 294) hydrogen bonds : angle 5.18375 / 3.66 ( 822) link_BETA1-4 : bond 0.00287 / 0.14 ( 2) link_BETA1-4 : angle 1.73521 / 0.89 ( 6) link_NAG-ASN : bond 0.00371 / 0.20 ( 1) link_NAG-ASN : angle 3.87885 / 2.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.194 Fit side-chains REVERT: A 84 ARG cc_start: 0.9092 (mtm-85) cc_final: 0.8814 (mpp-170) REVERT: A 89 GLN cc_start: 0.8299 (pp30) cc_final: 0.8029 (pm20) REVERT: B 122 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6442 (tp) REVERT: B 165 GLU cc_start: 0.7242 (mp0) cc_final: 0.6320 (mm-30) REVERT: H 33 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8405 (mtm-85) REVERT: H 66 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7630 (ttmt) REVERT: H 77 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7441 (ptpt) REVERT: H 111 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: C 386 LYS cc_start: 0.7990 (mmpt) cc_final: 0.7109 (tmmt) REVERT: L 24 GLN cc_start: 0.8060 (pt0) cc_final: 0.7673 (mt0) REVERT: L 70 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7594 (mp0) outliers start: 15 outliers final: 8 residues processed: 87 average time/residue: 0.5320 time to fit residues: 49.0354 Evaluate side-chains 90 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.193852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144640 restraints weight = 8916.309| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.61 r_work: 0.3126 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8304 Z= 0.218 Angle : 0.616 8.586 11322 Z= 0.309 Chirality : 0.046 0.156 1263 Planarity : 0.004 0.043 1451 Dihedral : 4.716 19.455 1203 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.55 % Allowed : 14.43 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.26), residues: 1051 helix: -1.90 (0.61), residues: 55 sheet: 0.50 (0.24), residues: 466 loop : -0.01 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 18 TYR 0.020 0.002 TYR B 177 PHE 0.014 0.002 PHE L 71 TRP 0.013 0.002 TRP A 36 HIS 0.005 0.001 HIS L 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.22 ( 8289) covalent geometry : angle 0.60887 / 0.31 (11289) SS BOND : bond 0.00429 / 0.30 ( 12) SS BOND : angle 0.96387 / 0.65 ( 24) hydrogen bonds : bond 0.03166 / 2.09 ( 294) hydrogen bonds : angle 5.48983 / 3.86 ( 822) link_BETA1-4 : bond 0.00343 / 0.18 ( 2) link_BETA1-4 : angle 2.00037 / 1.04 ( 6) link_NAG-ASN : bond 0.00846 / 0.45 ( 1) link_NAG-ASN : angle 4.40211 / 2.53 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.297 Fit side-chains REVERT: A 84 ARG cc_start: 0.9081 (mtm-85) cc_final: 0.8753 (mpp-170) REVERT: A 89 GLN cc_start: 0.8388 (pp30) cc_final: 0.8062 (pm20) REVERT: B 122 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6429 (tp) REVERT: B 165 GLU cc_start: 0.7317 (mp0) cc_final: 0.6386 (mm-30) REVERT: H 66 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7679 (ttmt) REVERT: H 77 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7730 (ptpt) REVERT: H 111 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: C 386 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7145 (tmmt) REVERT: L 24 GLN cc_start: 0.8103 (pt0) cc_final: 0.7685 (mt0) REVERT: L 70 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7711 (mp0) outliers start: 14 outliers final: 9 residues processed: 89 average time/residue: 0.5125 time to fit residues: 48.6483 Evaluate side-chains 92 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 111 GLN Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 18 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 98 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.195504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.142131 restraints weight = 8873.481| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.55 r_work: 0.3149 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8304 Z= 0.148 Angle : 0.572 7.545 11322 Z= 0.287 Chirality : 0.044 0.154 1263 Planarity : 0.004 0.046 1451 Dihedral : 4.555 19.324 1203 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.66 % Allowed : 14.43 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.26), residues: 1051 helix: -1.81 (0.63), residues: 55 sheet: 0.85 (0.25), residues: 431 loop : -0.02 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 18 TYR 0.021 0.001 TYR B 177 PHE 0.011 0.001 PHE A 111 TRP 0.011 0.001 TRP A 36 HIS 0.003 0.001 HIS L 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 8289) covalent geometry : angle 0.56632 / 0.29 (11289) SS BOND : bond 0.00300 / 0.21 ( 12) SS BOND : angle 0.80968 / 0.55 ( 24) hydrogen bonds : bond 0.02823 / 1.86 ( 294) hydrogen bonds : angle 5.29878 / 3.73 ( 822) link_BETA1-4 : bond 0.00261 / 0.13 ( 2) link_BETA1-4 : angle 1.84274 / 0.95 ( 6) link_NAG-ASN : bond 0.00514 / 0.27 ( 1) link_NAG-ASN : angle 3.91539 / 2.24 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3013.80 seconds wall clock time: 52 minutes 2.61 seconds (3122.61 seconds total)