Starting phenix.real_space_refine on Wed Mar 4 18:58:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xda_33140/03_2026/7xda_33140.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xda_33140/03_2026/7xda_33140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xda_33140/03_2026/7xda_33140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xda_33140/03_2026/7xda_33140.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xda_33140/03_2026/7xda_33140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xda_33140/03_2026/7xda_33140.map" } resolution = 2.98 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= 0.002 sd= 0.056 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: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 5110 2.51 5 N 1365 2.21 5 O 1579 1.98 5 H 7646 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15729 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3154 Classifications: {'peptide': 220} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 207} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 3138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3138 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 201} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2996 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 183} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3265 Classifications: {'peptide': 227} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 212} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3176 Classifications: {'peptide': 214} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 3.08, per 1000 atoms: 0.20 Number of scatterers: 15729 At special positions: 0 Unit cell: (133.98, 115.5, 129.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 1579 8.00 N 1365 7.00 C 5110 6.00 H 7646 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.04 Simple disulfide: pdb=" SG CYS B 141 " - pdb=" SG CYS B 197 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 361 " - pdb=" SG CYS A 414 " distance=2.03 Simple disulfide: pdb=" SG CYS A 462 " - pdb=" SG CYS A 470 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 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 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 475.1 milliseconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 26 sheets defined 7.7% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.518A pdb=" N ASP B 89 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 90 " --> pdb=" O ALA B 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 90' Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 122 through 130 removed outlier: 3.754A pdb=" N THR C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 Processing helix chain 'A' and resid 320 through 325 removed outlier: 3.850A pdb=" N PHE A 324 " --> pdb=" O PHE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 removed outlier: 4.004A pdb=" N TRP A 335 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 3.551A pdb=" N TYR A 351 " --> pdb=" O TYR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.648A pdb=" N TYR A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 399 through 404' Processing helix chain 'A' and resid 420 through 425 removed outlier: 3.565A pdb=" N SER A 425 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.636A pdb=" N THR D 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 198 removed outlier: 4.135A pdb=" N GLY D 198 " --> pdb=" O SER D 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 195 through 198' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.514A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 removed outlier: 3.556A pdb=" N LEU E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 188 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 8 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.777A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER B 40 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU B 45 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 121 through 125 removed outlier: 5.994A pdb=" N TYR B 177 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 125 removed outlier: 5.994A pdb=" N TYR B 177 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 155 removed outlier: 3.848A pdb=" N LYS B 210 " --> pdb=" O CYS B 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA8, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.646A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR C 98 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.646A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 115 through 119 removed outlier: 6.026A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 145 through 150 Processing sheet with id=AB3, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AB4, first strand: chain 'A' and resid 343 through 344 removed outlier: 6.327A pdb=" N CYS A 343 " --> pdb=" O CYS A 507 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 434 through 436 Processing sheet with id=AB6, first strand: chain 'A' and resid 455 through 456 Processing sheet with id=AB7, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.465A pdb=" N GLU D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE D 35 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE D 51 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.465A pdb=" N GLU D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU D 110 " --> pdb=" O ARG D 99 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.076A pdb=" N TYR D 184 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.076A pdb=" N TYR D 184 " --> pdb=" O ASP D 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AC4, first strand: chain 'E' and resid 4 through 7 removed outlier: 5.887A pdb=" N THR E 69 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N GLN E 27 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N SER E 67 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 11.555A pdb=" N ILE E 29 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 11.230A pdb=" N SER E 65 " --> pdb=" O ILE E 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 11 Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.703A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 116 through 118 Processing sheet with id=AC8, first strand: chain 'E' and resid 144 through 150 336 hydrogen bonds defined for protein. 831 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: 4.23 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7646 1.03 - 1.23: 231 1.23 - 1.43: 3377 1.43 - 1.63: 4648 1.63 - 1.83: 33 Bond restraints: 15935 Sorted by residual: bond pdb=" N ASN A 316 " pdb=" H1 ASN A 316 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N GLU B 1 " pdb=" H2 GLU B 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N GLU D 1 " pdb=" H3 GLU D 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N ASP E 1 " pdb=" H2 ASP E 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N GLU B 1 " pdb=" H3 GLU B 1 " ideal model delta sigma weight residual 0.890 0.959 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 15930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 20.97: 28660 20.97 - 41.94: 1 41.94 - 62.92: 0 62.92 - 83.89: 1 83.89 - 104.86: 3 Bond angle restraints: 28665 Sorted by residual: angle pdb=" H1 GLU B 1 " pdb=" N GLU B 1 " pdb=" H2 GLU B 1 " ideal model delta sigma weight residual 109.47 4.61 104.86 3.00e+00 1.11e-01 1.22e+03 angle pdb=" H1 ASP E 1 " pdb=" N ASP E 1 " pdb=" H2 ASP E 1 " ideal model delta sigma weight residual 109.47 5.86 103.61 3.00e+00 1.11e-01 1.19e+03 angle pdb=" H1 GLU C 1 " pdb=" N GLU C 1 " pdb=" H2 GLU C 1 " ideal model delta sigma weight residual 109.47 6.75 102.72 3.00e+00 1.11e-01 1.17e+03 angle pdb=" H1 GLU D 1 " pdb=" N GLU D 1 " pdb=" H3 GLU D 1 " ideal model delta sigma weight residual 109.47 25.94 83.53 3.00e+00 1.11e-01 7.75e+02 angle pdb=" H1 GLU D 1 " pdb=" N GLU D 1 " pdb=" H2 GLU D 1 " ideal model delta sigma weight residual 109.47 84.18 25.29 3.00e+00 1.11e-01 7.11e+01 ... (remaining 28660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6792 17.99 - 35.97: 631 35.97 - 53.96: 240 53.96 - 71.94: 51 71.94 - 89.93: 13 Dihedral angle restraints: 7727 sinusoidal: 4040 harmonic: 3687 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 41.74 51.26 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CA SER C 30 " pdb=" C SER C 30 " pdb=" N SER C 31 " pdb=" CA SER C 31 " ideal model delta harmonic sigma weight residual -180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 97 " pdb=" CB CYS D 97 " ideal model delta sinusoidal sigma weight residual 93.00 56.81 36.19 1 1.00e+01 1.00e-02 1.85e+01 ... (remaining 7724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 679 0.028 - 0.057: 380 0.057 - 0.085: 70 0.085 - 0.114: 80 0.114 - 0.142: 25 Chirality restraints: 1234 Sorted by residual: chirality pdb=" CA ILE E 106 " pdb=" N ILE E 106 " pdb=" C ILE E 106 " pdb=" CB ILE E 106 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE E 21 " pdb=" N ILE E 21 " pdb=" C ILE E 21 " pdb=" CB ILE E 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA VAL A 383 " pdb=" N VAL A 383 " pdb=" C VAL A 383 " pdb=" CB VAL A 383 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1231 not shown) Planarity restraints: 2464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 132 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C LEU D 132 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU D 132 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA D 133 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 156 " -0.024 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO D 157 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 157 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 157 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 149 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO B 150 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " -0.016 5.00e-02 4.00e+02 ... (remaining 2461 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 893 2.18 - 2.79: 30589 2.79 - 3.39: 38015 3.39 - 4.00: 54540 4.00 - 4.60: 83451 Nonbonded interactions: 207488 Sorted by model distance: nonbonded pdb=" HG SER A 420 " pdb=" OD2 ASP A 424 " model vdw 1.577 2.450 nonbonded pdb=" HH TYR E 36 " pdb=" OE1 GLN E 89 " model vdw 1.611 2.450 nonbonded pdb=" O HIS C 190 " pdb=" HE ARG C 212 " model vdw 1.635 2.450 nonbonded pdb=" HZ2 LYS A 440 " pdb=" O GLN A 456 " model vdw 1.635 2.450 nonbonded pdb=" HG SER B 131 " pdb=" O ILE C 118 " model vdw 1.649 2.450 ... (remaining 207483 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: 12.790 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: 0.110 Extract box with map and model: 0.520 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.850 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:7.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.005 0.051 8300 Z= 0.190 Angle : 0.544 4.209 11305 Z= 0.297 Chirality : 0.043 0.142 1234 Planarity : 0.003 0.036 1458 Dihedral : 16.341 89.930 2922 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.31 % Favored : 93.59 % Rotamer: Outliers : 1.85 % Allowed : 24.07 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -3.63 (0.22), residues: 1061 helix: -4.52 (0.30), residues: 55 sheet: -1.20 (0.22), residues: 472 loop : -3.40 (0.20), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 339 TYR 0.018 0.001 TYR E 91 PHE 0.011 0.001 PHE B 78 TRP 0.010 0.001 TRP D 84 HIS 0.003 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 8289) covalent geometry : angle 0.54312 (11283) SS BOND : bond 0.00384 ( 11) SS BOND : angle 0.98018 ( 22) hydrogen bonds : bond 0.13982 ( 291) hydrogen bonds : angle 6.76841 ( 831) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.7989 (tt0) cc_final: 0.7720 (tt0) REVERT: B 200 ASN cc_start: 0.6195 (t0) cc_final: 0.5929 (p0) REVERT: B 209 ASP cc_start: 0.7886 (m-30) cc_final: 0.7627 (m-30) REVERT: A 450 ILE cc_start: 0.8629 (pt) cc_final: 0.8127 (mm) REVERT: D 163 ASN cc_start: 0.6396 (t0) cc_final: 0.5823 (t0) REVERT: E 161 GLU cc_start: 0.6892 (pm20) cc_final: 0.6667 (pm20) outliers start: 16 outliers final: 7 residues processed: 147 average time/residue: 1.1040 time to fit residues: 173.3090 Evaluate side-chains 102 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 214 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN B 50 GLN B 58 ASN B 165 HIS C 138 ASN C 161 GLN A 370 ASN E 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.173450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113052 restraints weight = 27890.458| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.08 r_work: 0.3148 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8300 Z= 0.127 Angle : 0.538 6.396 11305 Z= 0.279 Chirality : 0.044 0.178 1234 Planarity : 0.004 0.053 1458 Dihedral : 5.040 30.471 1164 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.66 % Favored : 94.25 % Rotamer: Outliers : 1.97 % Allowed : 26.97 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -2.69 (0.23), residues: 1061 helix: -3.90 (0.43), residues: 54 sheet: -0.64 (0.23), residues: 474 loop : -2.70 (0.22), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 143 TYR 0.016 0.001 TYR E 91 PHE 0.010 0.001 PHE B 78 TRP 0.009 0.001 TRP D 111 HIS 0.003 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8289) covalent geometry : angle 0.53418 (11283) SS BOND : bond 0.00534 ( 11) SS BOND : angle 1.60004 ( 22) hydrogen bonds : bond 0.03267 ( 291) hydrogen bonds : angle 5.71726 ( 831) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8422 (tt0) cc_final: 0.8135 (tt0) REVERT: B 209 ASP cc_start: 0.7918 (m-30) cc_final: 0.7610 (m-30) REVERT: C 79 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.8000 (mp) REVERT: C 193 TYR cc_start: 0.6547 (m-80) cc_final: 0.5882 (m-80) REVERT: A 450 ILE cc_start: 0.8874 (pt) cc_final: 0.8320 (mm) REVERT: D 163 ASN cc_start: 0.6775 (t0) cc_final: 0.6133 (t0) REVERT: E 161 GLU cc_start: 0.7058 (pm20) cc_final: 0.6723 (pm20) outliers start: 17 outliers final: 7 residues processed: 119 average time/residue: 1.0458 time to fit residues: 133.5189 Evaluate side-chains 103 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 1 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 16 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 59 optimal weight: 0.0020 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 98 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 58 ASN C 139 ASN C 161 GLN E 166 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.174574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113822 restraints weight = 28199.699| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.10 r_work: 0.3150 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8300 Z= 0.101 Angle : 0.503 5.172 11305 Z= 0.260 Chirality : 0.043 0.163 1234 Planarity : 0.004 0.037 1458 Dihedral : 4.551 29.785 1156 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 2.08 % Allowed : 26.27 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -1.99 (0.24), residues: 1061 helix: -3.64 (0.47), residues: 56 sheet: -0.17 (0.24), residues: 470 loop : -2.18 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 TYR 0.014 0.001 TYR A 471 PHE 0.012 0.001 PHE E 139 TRP 0.008 0.001 TRP D 84 HIS 0.002 0.001 HIS B 53 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8289) covalent geometry : angle 0.49806 (11283) SS BOND : bond 0.00435 ( 11) SS BOND : angle 1.63710 ( 22) hydrogen bonds : bond 0.02902 ( 291) hydrogen bonds : angle 5.35213 ( 831) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8436 (tt0) cc_final: 0.8112 (tt0) REVERT: B 209 ASP cc_start: 0.7955 (m-30) cc_final: 0.7648 (m-30) REVERT: C 79 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7982 (mp) REVERT: C 193 TYR cc_start: 0.6428 (m-80) cc_final: 0.5750 (m-80) REVERT: A 450 ILE cc_start: 0.8900 (pt) cc_final: 0.8344 (mm) REVERT: D 163 ASN cc_start: 0.6761 (t0) cc_final: 0.6142 (t0) REVERT: E 161 GLU cc_start: 0.7093 (pm20) cc_final: 0.6734 (pm20) outliers start: 18 outliers final: 9 residues processed: 114 average time/residue: 1.0607 time to fit residues: 129.2958 Evaluate side-chains 103 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain D residue 187 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 21 optimal weight: 0.0870 chunk 52 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.173461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112895 restraints weight = 27862.647| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.08 r_work: 0.3140 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8300 Z= 0.104 Angle : 0.492 4.992 11305 Z= 0.255 Chirality : 0.043 0.172 1234 Planarity : 0.004 0.036 1458 Dihedral : 4.502 31.225 1156 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 1.16 % Allowed : 27.20 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -1.60 (0.25), residues: 1061 helix: -3.49 (0.50), residues: 56 sheet: 0.03 (0.24), residues: 466 loop : -1.81 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 143 TYR 0.013 0.001 TYR E 91 PHE 0.015 0.001 PHE E 139 TRP 0.007 0.001 TRP D 84 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8289) covalent geometry : angle 0.48953 (11283) SS BOND : bond 0.00425 ( 11) SS BOND : angle 1.24195 ( 22) hydrogen bonds : bond 0.02718 ( 291) hydrogen bonds : angle 5.18957 ( 831) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8447 (tt0) cc_final: 0.8132 (tt0) REVERT: B 209 ASP cc_start: 0.7964 (m-30) cc_final: 0.7623 (m-30) REVERT: C 79 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7961 (mp) REVERT: C 193 TYR cc_start: 0.6452 (m-80) cc_final: 0.5817 (m-80) REVERT: A 450 ILE cc_start: 0.8915 (pt) cc_final: 0.8370 (mm) REVERT: D 163 ASN cc_start: 0.6802 (t0) cc_final: 0.6187 (t0) REVERT: E 137 ASN cc_start: 0.8005 (m-40) cc_final: 0.7737 (m-40) REVERT: E 161 GLU cc_start: 0.7157 (pm20) cc_final: 0.6816 (pm20) outliers start: 10 outliers final: 7 residues processed: 105 average time/residue: 1.0196 time to fit residues: 115.0253 Evaluate side-chains 96 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 139 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.0670 chunk 47 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN E 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.170129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108793 restraints weight = 27956.364| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.08 r_work: 0.3081 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8300 Z= 0.194 Angle : 0.567 6.248 11305 Z= 0.297 Chirality : 0.045 0.173 1234 Planarity : 0.004 0.035 1458 Dihedral : 4.979 36.646 1156 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.75 % Favored : 94.16 % Rotamer: Outliers : 2.43 % Allowed : 26.16 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -1.46 (0.25), residues: 1061 helix: -3.53 (0.49), residues: 56 sheet: 0.08 (0.24), residues: 475 loop : -1.69 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 143 TYR 0.021 0.002 TYR E 173 PHE 0.056 0.002 PHE E 139 TRP 0.009 0.002 TRP D 48 HIS 0.003 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 8289) covalent geometry : angle 0.56216 (11283) SS BOND : bond 0.00599 ( 11) SS BOND : angle 1.76627 ( 22) hydrogen bonds : bond 0.03282 ( 291) hydrogen bonds : angle 5.39194 ( 831) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8477 (tt0) cc_final: 0.8182 (tt0) REVERT: B 209 ASP cc_start: 0.7975 (m-30) cc_final: 0.7658 (m-30) REVERT: C 7 SER cc_start: 0.6650 (OUTLIER) cc_final: 0.6442 (p) REVERT: C 24 ARG cc_start: 0.7973 (ttt180) cc_final: 0.7766 (ttm110) REVERT: C 79 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.8001 (mp) REVERT: C 193 TYR cc_start: 0.6565 (m-80) cc_final: 0.5953 (m-80) REVERT: A 450 ILE cc_start: 0.8955 (pt) cc_final: 0.8390 (mm) REVERT: D 163 ASN cc_start: 0.6781 (t0) cc_final: 0.6165 (t0) REVERT: E 161 GLU cc_start: 0.7237 (pm20) cc_final: 0.6883 (pm20) outliers start: 21 outliers final: 13 residues processed: 113 average time/residue: 1.0714 time to fit residues: 129.7083 Evaluate side-chains 108 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 139 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 58 ASN C 161 GLN E 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.171296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110141 restraints weight = 27867.056| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.08 r_work: 0.3101 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8300 Z= 0.125 Angle : 0.510 5.273 11305 Z= 0.264 Chirality : 0.044 0.175 1234 Planarity : 0.004 0.045 1458 Dihedral : 4.738 37.306 1156 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.00 % Rotamer: Outliers : 2.89 % Allowed : 26.74 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -1.21 (0.25), residues: 1061 helix: -3.34 (0.54), residues: 50 sheet: 0.26 (0.24), residues: 465 loop : -1.53 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 24 TYR 0.016 0.001 TYR E 91 PHE 0.016 0.001 PHE E 139 TRP 0.008 0.001 TRP D 48 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8289) covalent geometry : angle 0.50790 (11283) SS BOND : bond 0.00430 ( 11) SS BOND : angle 1.20687 ( 22) hydrogen bonds : bond 0.02796 ( 291) hydrogen bonds : angle 5.21978 ( 831) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.422 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: B 46 GLU cc_start: 0.8463 (tt0) cc_final: 0.8142 (tt0) REVERT: B 209 ASP cc_start: 0.8017 (m-30) cc_final: 0.7757 (m-30) REVERT: C 79 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.8021 (mp) REVERT: C 193 TYR cc_start: 0.6553 (m-80) cc_final: 0.5959 (m-80) REVERT: A 450 ILE cc_start: 0.8946 (pt) cc_final: 0.8409 (mm) REVERT: D 163 ASN cc_start: 0.6770 (t0) cc_final: 0.6147 (t0) REVERT: E 161 GLU cc_start: 0.7265 (pm20) cc_final: 0.6897 (pm20) outliers start: 25 outliers final: 14 residues processed: 118 average time/residue: 0.9343 time to fit residues: 118.8233 Evaluate side-chains 105 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 93 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 38 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 58 ASN C 161 GLN E 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.169922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108587 restraints weight = 27714.890| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.07 r_work: 0.3084 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8300 Z= 0.158 Angle : 0.529 5.340 11305 Z= 0.275 Chirality : 0.044 0.176 1234 Planarity : 0.004 0.060 1458 Dihedral : 4.830 39.769 1156 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.75 % Favored : 94.16 % Rotamer: Outliers : 2.55 % Allowed : 26.85 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -1.14 (0.25), residues: 1061 helix: -3.29 (0.55), residues: 50 sheet: 0.31 (0.24), residues: 465 loop : -1.48 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 24 TYR 0.019 0.001 TYR E 91 PHE 0.009 0.001 PHE E 94 TRP 0.009 0.001 TRP D 48 HIS 0.003 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8289) covalent geometry : angle 0.52599 (11283) SS BOND : bond 0.00477 ( 11) SS BOND : angle 1.39250 ( 22) hydrogen bonds : bond 0.03096 ( 291) hydrogen bonds : angle 5.29067 ( 831) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.544 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: B 46 GLU cc_start: 0.8476 (tt0) cc_final: 0.8190 (tt0) REVERT: B 209 ASP cc_start: 0.8002 (m-30) cc_final: 0.7730 (m-30) REVERT: C 79 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8021 (mp) REVERT: C 193 TYR cc_start: 0.6541 (m-80) cc_final: 0.5995 (m-80) REVERT: A 450 ILE cc_start: 0.8955 (pt) cc_final: 0.8415 (mm) REVERT: D 163 ASN cc_start: 0.6774 (t0) cc_final: 0.6159 (t0) REVERT: D 214 LYS cc_start: 0.7535 (mtpt) cc_final: 0.6689 (tmtm) REVERT: E 161 GLU cc_start: 0.7257 (pm20) cc_final: 0.6890 (pm20) outliers start: 22 outliers final: 18 residues processed: 110 average time/residue: 1.0268 time to fit residues: 121.4928 Evaluate side-chains 109 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 170 LYS Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 1 ASP Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 121 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.0870 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 92 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 overall best weight: 0.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 58 ASN C 161 GLN E 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.171927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110852 restraints weight = 27935.459| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.09 r_work: 0.3113 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8300 Z= 0.098 Angle : 0.493 5.126 11305 Z= 0.254 Chirality : 0.043 0.172 1234 Planarity : 0.004 0.063 1458 Dihedral : 4.581 38.860 1156 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 2.31 % Allowed : 27.20 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -0.93 (0.25), residues: 1061 helix: -3.22 (0.55), residues: 50 sheet: 0.48 (0.24), residues: 464 loop : -1.36 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 24 TYR 0.013 0.001 TYR E 91 PHE 0.013 0.001 PHE E 139 TRP 0.007 0.001 TRP D 84 HIS 0.002 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8289) covalent geometry : angle 0.49202 (11283) SS BOND : bond 0.00334 ( 11) SS BOND : angle 0.95685 ( 22) hydrogen bonds : bond 0.02611 ( 291) hydrogen bonds : angle 5.07774 ( 831) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8456 (tt0) cc_final: 0.8142 (tt0) REVERT: B 209 ASP cc_start: 0.7992 (m-30) cc_final: 0.7696 (m-30) REVERT: C 79 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7980 (mp) REVERT: C 193 TYR cc_start: 0.6515 (m-80) cc_final: 0.5987 (m-80) REVERT: A 450 ILE cc_start: 0.8948 (pt) cc_final: 0.8417 (mm) REVERT: D 163 ASN cc_start: 0.6764 (t0) cc_final: 0.6175 (t0) REVERT: D 214 LYS cc_start: 0.7530 (mtpt) cc_final: 0.6684 (tmtm) REVERT: E 161 GLU cc_start: 0.7266 (pm20) cc_final: 0.6893 (pm20) outliers start: 20 outliers final: 15 residues processed: 110 average time/residue: 0.9854 time to fit residues: 116.7140 Evaluate side-chains 105 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 121 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 58 ASN C 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.169822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108504 restraints weight = 28033.851| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.08 r_work: 0.3079 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8300 Z= 0.166 Angle : 0.533 5.227 11305 Z= 0.277 Chirality : 0.045 0.178 1234 Planarity : 0.004 0.066 1458 Dihedral : 4.801 41.309 1156 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.84 % Favored : 94.06 % Rotamer: Outliers : 2.55 % Allowed : 26.62 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -0.94 (0.25), residues: 1061 helix: -3.26 (0.55), residues: 50 sheet: 0.48 (0.24), residues: 464 loop : -1.37 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 24 TYR 0.019 0.001 TYR E 91 PHE 0.009 0.001 PHE E 94 TRP 0.008 0.001 TRP D 48 HIS 0.003 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8289) covalent geometry : angle 0.53000 (11283) SS BOND : bond 0.00504 ( 11) SS BOND : angle 1.47222 ( 22) hydrogen bonds : bond 0.03084 ( 291) hydrogen bonds : angle 5.24561 ( 831) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8479 (tt0) cc_final: 0.8197 (tt0) REVERT: B 209 ASP cc_start: 0.7969 (m-30) cc_final: 0.7706 (m-30) REVERT: C 193 TYR cc_start: 0.6515 (m-80) cc_final: 0.5990 (m-80) REVERT: A 450 ILE cc_start: 0.8971 (pt) cc_final: 0.8423 (mm) REVERT: A 466 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7733 (mt-10) REVERT: D 163 ASN cc_start: 0.6761 (t0) cc_final: 0.6173 (t0) REVERT: D 214 LYS cc_start: 0.7540 (mtpt) cc_final: 0.6728 (tmtm) REVERT: E 107 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7573 (ttmt) outliers start: 22 outliers final: 14 residues processed: 110 average time/residue: 1.0479 time to fit residues: 123.8251 Evaluate side-chains 106 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 121 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 51 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 ASN C 161 GLN D 207 ASN E 137 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.170896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109676 restraints weight = 27907.350| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.08 r_work: 0.3086 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8300 Z= 0.123 Angle : 0.517 5.368 11305 Z= 0.266 Chirality : 0.044 0.176 1234 Planarity : 0.005 0.068 1458 Dihedral : 4.719 41.528 1156 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.72 % Rotamer: Outliers : 1.85 % Allowed : 27.43 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -0.82 (0.25), residues: 1061 helix: -3.25 (0.55), residues: 50 sheet: 0.58 (0.25), residues: 459 loop : -1.29 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 24 TYR 0.016 0.001 TYR E 91 PHE 0.012 0.001 PHE E 139 TRP 0.008 0.001 TRP D 48 HIS 0.003 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8289) covalent geometry : angle 0.51433 (11283) SS BOND : bond 0.00394 ( 11) SS BOND : angle 1.18929 ( 22) hydrogen bonds : bond 0.02818 ( 291) hydrogen bonds : angle 5.14984 ( 831) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 54 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue THR 86 is missing expected H atoms. Skipping. Residue SER 116 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue LYS 144 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 170 is missing expected H atoms. Skipping. Residue SER 173 is missing expected H atoms. Skipping. Residue SER 174 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue VAL 182 is missing expected H atoms. Skipping. Residue THR 194 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue SER 64 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 130 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue VAL 151 is missing expected H atoms. Skipping. Residue VAL 164 is missing expected H atoms. Skipping. Residue THR 165 is missing expected H atoms. Skipping. Residue SER 169 is missing expected H atoms. Skipping. Residue LEU 176 is missing expected H atoms. Skipping. Residue THR 207 is missing expected H atoms. Skipping. Residue TYR 351 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue SER 86 is missing expected H atoms. Skipping. Residue MET 94 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue LEU 146 is missing expected H atoms. Skipping. Residue LEU 149 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue THR 173 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue ILE 203 is missing expected H atoms. Skipping. Residue SER 77 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue VAL 150 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 GLU cc_start: 0.8470 (tt0) cc_final: 0.8151 (tt0) REVERT: B 209 ASP cc_start: 0.7936 (m-30) cc_final: 0.7685 (m-30) REVERT: C 193 TYR cc_start: 0.6506 (m-80) cc_final: 0.5979 (m-80) REVERT: A 450 ILE cc_start: 0.8962 (pt) cc_final: 0.8425 (mm) REVERT: D 163 ASN cc_start: 0.6783 (t0) cc_final: 0.6186 (t0) REVERT: D 214 LYS cc_start: 0.7526 (mtpt) cc_final: 0.6690 (tmtm) REVERT: E 81 ASP cc_start: 0.8510 (t0) cc_final: 0.8164 (t0) REVERT: E 107 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7555 (ttmt) outliers start: 16 outliers final: 14 residues processed: 105 average time/residue: 1.0666 time to fit residues: 119.9043 Evaluate side-chains 103 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 121 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 78 optimal weight: 0.0000 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.170274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108999 restraints weight = 27854.110| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.07 r_work: 0.3077 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8300 Z= 0.171 Angle : 0.544 5.351 11305 Z= 0.281 Chirality : 0.045 0.179 1234 Planarity : 0.005 0.066 1458 Dihedral : 4.876 43.849 1156 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 2.31 % Allowed : 27.08 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.10 % 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: -0.78 (0.25), residues: 1061 helix: -3.03 (0.61), residues: 44 sheet: 0.55 (0.25), residues: 461 loop : -1.26 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 24 TYR 0.020 0.002 TYR E 91 PHE 0.009 0.001 PHE E 94 TRP 0.009 0.001 TRP D 48 HIS 0.003 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8289) covalent geometry : angle 0.54105 (11283) SS BOND : bond 0.00499 ( 11) SS BOND : angle 1.43649 ( 22) hydrogen bonds : bond 0.03139 ( 291) hydrogen bonds : angle 5.27193 ( 831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6815.03 seconds wall clock time: 115 minutes 49.21 seconds (6949.21 seconds total)