Starting phenix.real_space_refine on Thu Feb 5 11:54:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ipn_60778/02_2026/9ipn_60778_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ipn_60778/02_2026/9ipn_60778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ipn_60778/02_2026/9ipn_60778_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ipn_60778/02_2026/9ipn_60778_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ipn_60778/02_2026/9ipn_60778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ipn_60778/02_2026/9ipn_60778.map" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 78 5.16 5 C 5700 2.51 5 N 1332 2.21 5 O 1446 1.98 5 H 7998 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16560 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2705 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain breaks: 1 Chain: "B" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2705 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain breaks: 1 Chain: "F" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2705 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain breaks: 1 Chain: "C" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2705 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain breaks: 1 Chain: "D" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2705 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain breaks: 1 Chain: "E" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2705 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain breaks: 1 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'C14': 1, 'MC3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'C14': 1, 'MC3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'C14': 1, 'MC3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'C14': 1, 'MC3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'C14': 1, 'MC3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'C14': 1, 'MC3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Time building chain proxies: 2.86, per 1000 atoms: 0.17 Number of scatterers: 16560 At special positions: 0 Unit cell: (103.68, 95.58, 82.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 6 15.00 O 1446 8.00 N 1332 7.00 C 5700 6.00 H 7998 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " 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: 1.44 Conformation dependent library (CDL) restraints added in 423.0 milliseconds 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 73.4% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 19 through 46 removed outlier: 5.424A pdb=" N GLU A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N THR A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 74 through 101 Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 246 through 276 Processing helix chain 'B' and resid 20 through 46 removed outlier: 5.405A pdb=" N GLU B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N THR B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 74 through 101 Proline residue: B 89 - end of helix Processing helix chain 'B' and resid 195 through 222 Processing helix chain 'B' and resid 246 through 276 Processing helix chain 'F' and resid 20 through 46 removed outlier: 5.422A pdb=" N GLU F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N THR F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 71 Processing helix chain 'F' and resid 74 through 101 Proline residue: F 89 - end of helix Processing helix chain 'F' and resid 195 through 222 Processing helix chain 'F' and resid 246 through 275 Processing helix chain 'C' and resid 20 through 46 removed outlier: 5.419A pdb=" N GLU C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N THR C 44 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 74 through 101 Proline residue: C 89 - end of helix Processing helix chain 'C' and resid 195 through 222 Processing helix chain 'C' and resid 246 through 275 Processing helix chain 'D' and resid 20 through 46 removed outlier: 5.421A pdb=" N GLU D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N THR D 44 " --> pdb=" O ILE D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 74 through 101 Proline residue: D 89 - end of helix Processing helix chain 'D' and resid 195 through 222 Processing helix chain 'D' and resid 246 through 276 Processing helix chain 'E' and resid 20 through 46 removed outlier: 5.404A pdb=" N GLU E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N THR E 44 " --> pdb=" O ILE E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 74 through 101 Proline residue: E 89 - end of helix Processing helix chain 'E' and resid 195 through 222 Processing helix chain 'E' and resid 246 through 276 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'F' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'E' and resid 54 through 55 635 hydrogen bonds defined for protein. 1869 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 1.96 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: 7980 1.03 - 1.23: 86 1.23 - 1.42: 3598 1.42 - 1.61: 4974 1.61 - 1.81: 114 Bond restraints: 16752 Sorted by residual: bond pdb=" C11 MC3 D 401 " pdb=" O3 MC3 D 401 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C11 MC3 A 401 " pdb=" O3 MC3 A 401 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C11 MC3 F 401 " pdb=" O3 MC3 F 401 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C11 MC3 B 401 " pdb=" O3 MC3 B 401 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C11 MC3 E 401 " pdb=" O3 MC3 E 401 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 16747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 29781 5.65 - 11.30: 57 11.30 - 16.96: 6 16.96 - 22.61: 0 22.61 - 28.26: 18 Bond angle restraints: 29862 Sorted by residual: angle pdb=" CG2 THR D 20 " pdb=" CB THR D 20 " pdb=" HB THR D 20 " ideal model delta sigma weight residual 108.00 79.74 28.26 3.00e+00 1.11e-01 8.87e+01 angle pdb=" CG2 THR B 20 " pdb=" CB THR B 20 " pdb=" HB THR B 20 " ideal model delta sigma weight residual 108.00 79.92 28.08 3.00e+00 1.11e-01 8.76e+01 angle pdb=" CG2 THR E 20 " pdb=" CB THR E 20 " pdb=" HB THR E 20 " ideal model delta sigma weight residual 108.00 79.94 28.06 3.00e+00 1.11e-01 8.75e+01 angle pdb=" CG2 THR C 20 " pdb=" CB THR C 20 " pdb=" HB THR C 20 " ideal model delta sigma weight residual 108.00 80.09 27.91 3.00e+00 1.11e-01 8.66e+01 angle pdb=" CG2 THR F 20 " pdb=" CB THR F 20 " pdb=" HB THR F 20 " ideal model delta sigma weight residual 108.00 80.32 27.68 3.00e+00 1.11e-01 8.51e+01 ... (remaining 29857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.81: 7418 23.81 - 47.62: 544 47.62 - 71.43: 147 71.43 - 95.24: 3 95.24 - 119.05: 6 Dihedral angle restraints: 8118 sinusoidal: 4410 harmonic: 3708 Sorted by residual: dihedral pdb=" N MC3 B 401 " pdb=" C4 MC3 B 401 " pdb=" C5 MC3 B 401 " pdb=" O4P MC3 B 401 " ideal model delta sinusoidal sigma weight residual -70.18 48.87 -119.05 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" N MC3 E 401 " pdb=" C4 MC3 E 401 " pdb=" C5 MC3 E 401 " pdb=" O4P MC3 E 401 " ideal model delta sinusoidal sigma weight residual -70.18 48.86 -119.04 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" N MC3 A 401 " pdb=" C4 MC3 A 401 " pdb=" C5 MC3 A 401 " pdb=" O4P MC3 A 401 " ideal model delta sinusoidal sigma weight residual -70.18 48.82 -119.00 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 8115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 1332 0.270 - 0.541: 0 0.541 - 0.811: 0 0.811 - 1.081: 0 1.081 - 1.352: 6 Chirality restraints: 1338 Sorted by residual: chirality pdb=" CB THR A 20 " pdb=" CA THR A 20 " pdb=" OG1 THR A 20 " pdb=" CG2 THR A 20 " both_signs ideal model delta sigma weight residual False 2.55 1.20 1.35 2.00e-01 2.50e+01 4.57e+01 chirality pdb=" CB THR F 20 " pdb=" CA THR F 20 " pdb=" OG1 THR F 20 " pdb=" CG2 THR F 20 " both_signs ideal model delta sigma weight residual False 2.55 1.21 1.35 2.00e-01 2.50e+01 4.53e+01 chirality pdb=" CB THR C 20 " pdb=" CA THR C 20 " pdb=" OG1 THR C 20 " pdb=" CG2 THR C 20 " both_signs ideal model delta sigma weight residual False 2.55 1.24 1.31 2.00e-01 2.50e+01 4.27e+01 ... (remaining 1335 not shown) Planarity restraints: 2370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 24 " -0.190 9.50e-02 1.11e+02 6.34e-02 4.53e+00 pdb=" NE ARG C 24 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG C 24 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 24 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG C 24 " -0.007 2.00e-02 2.50e+03 pdb="HH11 ARG C 24 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG C 24 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C 24 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 24 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 24 " -0.153 9.50e-02 1.11e+02 5.12e-02 3.01e+00 pdb=" NE ARG D 24 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG D 24 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 24 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 24 " -0.007 2.00e-02 2.50e+03 pdb="HH11 ARG D 24 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG D 24 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 24 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 24 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 24 " 0.110 9.50e-02 1.11e+02 3.68e-02 1.78e+00 pdb=" NE ARG E 24 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG E 24 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG E 24 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 24 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG E 24 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG E 24 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG E 24 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG E 24 " 0.000 2.00e-02 2.50e+03 ... (remaining 2367 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 183 2.08 - 2.71: 25803 2.71 - 3.34: 48774 3.34 - 3.97: 60643 3.97 - 4.60: 94345 Nonbonded interactions: 229748 Sorted by model distance: nonbonded pdb=" O VAL A 203 " pdb="HD21 ASN A 207 " model vdw 1.448 2.450 nonbonded pdb=" O VAL D 203 " pdb="HD21 ASN D 207 " model vdw 1.449 2.450 nonbonded pdb=" H ASN D 207 " pdb="HD21 ASN D 207 " model vdw 1.690 2.100 nonbonded pdb=" H ASN A 207 " pdb="HD21 ASN A 207 " model vdw 1.697 2.100 nonbonded pdb=" HE ARG F 77 " pdb=" OE2 GLU E 249 " model vdw 1.735 2.450 ... (remaining 229743 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 14.830 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 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 : 0.007 0.072 8772 Z= 0.330 Angle : 1.047 16.522 11862 Z= 0.473 Chirality : 0.097 1.352 1338 Planarity : 0.005 0.084 1422 Dihedral : 17.896 119.052 3246 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.02 % Favored : 95.78 % Rotamer: Outliers : 0.22 % Allowed : 19.48 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.23), residues: 996 helix: 0.27 (0.17), residues: 744 sheet: -0.99 (0.45), residues: 102 loop : -0.77 (0.45), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 24 TYR 0.017 0.002 TYR E 67 PHE 0.008 0.001 PHE D 213 TRP 0.005 0.001 TRP F 79 HIS 0.007 0.002 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00737 ( 8754) covalent geometry : angle 1.04737 (11826) SS BOND : bond 0.00132 ( 18) SS BOND : angle 0.87871 ( 36) hydrogen bonds : bond 0.09894 ( 635) hydrogen bonds : angle 4.68511 ( 1869) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 278 ARG cc_start: 0.6785 (mmp80) cc_final: 0.6481 (mmp80) REVERT: F 273 ASN cc_start: 0.8406 (t0) cc_final: 0.7897 (t0) REVERT: C 273 ASN cc_start: 0.8383 (t0) cc_final: 0.7892 (t0) REVERT: D 273 ASN cc_start: 0.8239 (t0) cc_final: 0.7711 (t0) REVERT: E 273 ASN cc_start: 0.8413 (t0) cc_final: 0.7887 (t0) outliers start: 2 outliers final: 1 residues processed: 176 average time/residue: 1.1696 time to fit residues: 218.4854 Evaluate side-chains 172 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.111501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.080740 restraints weight = 31116.575| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.78 r_work: 0.2756 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8772 Z= 0.143 Angle : 0.635 10.953 11862 Z= 0.341 Chirality : 0.101 1.403 1338 Planarity : 0.004 0.077 1422 Dihedral : 14.185 128.398 1393 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.41 % Allowed : 18.29 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.26), residues: 996 helix: 1.82 (0.18), residues: 744 sheet: -0.35 (0.47), residues: 102 loop : -0.13 (0.48), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 24 TYR 0.013 0.001 TYR A 67 PHE 0.008 0.001 PHE D 53 TRP 0.002 0.001 TRP C 277 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8754) covalent geometry : angle 0.63488 (11826) SS BOND : bond 0.00080 ( 18) SS BOND : angle 0.66525 ( 36) hydrogen bonds : bond 0.04861 ( 635) hydrogen bonds : angle 3.89029 ( 1869) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 207 ASN cc_start: 0.8942 (m-40) cc_final: 0.8640 (m110) REVERT: A 233 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7848 (mmm-85) REVERT: F 273 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.7913 (t0) REVERT: C 273 ASN cc_start: 0.8413 (t0) cc_final: 0.7824 (t0) REVERT: D 273 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7661 (t0) REVERT: E 273 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8249 (m-40) outliers start: 13 outliers final: 4 residues processed: 172 average time/residue: 1.2028 time to fit residues: 219.5569 Evaluate side-chains 175 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 273 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.110288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.079566 restraints weight = 31593.238| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.78 r_work: 0.2747 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8772 Z= 0.199 Angle : 0.640 10.888 11862 Z= 0.345 Chirality : 0.100 1.374 1338 Planarity : 0.004 0.063 1422 Dihedral : 13.188 117.390 1393 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.73 % Allowed : 18.40 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.26), residues: 996 helix: 2.28 (0.18), residues: 744 sheet: -0.40 (0.46), residues: 102 loop : -0.06 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 24 TYR 0.014 0.002 TYR B 67 PHE 0.007 0.001 PHE A 53 TRP 0.004 0.001 TRP C 79 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 8754) covalent geometry : angle 0.63970 (11826) SS BOND : bond 0.00115 ( 18) SS BOND : angle 0.76694 ( 36) hydrogen bonds : bond 0.05040 ( 635) hydrogen bonds : angle 3.77971 ( 1869) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 233 ARG cc_start: 0.8216 (mmm-85) cc_final: 0.7930 (mmm-85) REVERT: A 273 ASN cc_start: 0.8296 (t0) cc_final: 0.8046 (m-40) REVERT: B 273 ASN cc_start: 0.8439 (t0) cc_final: 0.7829 (t0) REVERT: F 273 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.7902 (t0) REVERT: C 273 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.7899 (t0) REVERT: D 273 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7594 (t0) REVERT: E 273 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.7819 (t0) outliers start: 16 outliers final: 7 residues processed: 184 average time/residue: 1.0538 time to fit residues: 206.3409 Evaluate side-chains 185 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 273 ASN Chi-restraints excluded: chain D residue 90 SER Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 273 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 80 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 96 optimal weight: 0.3980 chunk 67 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 207 ASN C 207 ASN D 207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.114465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.084226 restraints weight = 31024.051| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.78 r_work: 0.2805 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8772 Z= 0.108 Angle : 0.593 11.009 11862 Z= 0.316 Chirality : 0.100 1.390 1338 Planarity : 0.003 0.053 1422 Dihedral : 12.315 104.963 1393 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.84 % Allowed : 18.18 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.97 (0.26), residues: 996 helix: 2.63 (0.18), residues: 744 sheet: -0.08 (0.47), residues: 102 loop : 0.01 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 24 TYR 0.012 0.001 TYR A 96 PHE 0.004 0.001 PHE D 53 TRP 0.006 0.001 TRP E 277 HIS 0.003 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8754) covalent geometry : angle 0.59292 (11826) SS BOND : bond 0.00092 ( 18) SS BOND : angle 0.60235 ( 36) hydrogen bonds : bond 0.04098 ( 635) hydrogen bonds : angle 3.54780 ( 1869) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 ASN cc_start: 0.8316 (t0) cc_final: 0.7626 (t0) REVERT: B 273 ASN cc_start: 0.8429 (t0) cc_final: 0.8198 (m-40) REVERT: F 273 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.7822 (t0) REVERT: C 273 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.7802 (t0) REVERT: D 273 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7577 (t0) REVERT: E 233 ARG cc_start: 0.8137 (mmm-85) cc_final: 0.7933 (mmm-85) REVERT: E 273 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8209 (m-40) outliers start: 17 outliers final: 4 residues processed: 188 average time/residue: 1.1188 time to fit residues: 223.6276 Evaluate side-chains 181 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 173 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain C residue 273 ASN Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain E residue 273 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN F 207 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN D 207 ASN E 207 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.111990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.080536 restraints weight = 30615.039| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.83 r_work: 0.2704 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8772 Z= 0.128 Angle : 0.600 10.985 11862 Z= 0.319 Chirality : 0.100 1.395 1338 Planarity : 0.003 0.041 1422 Dihedral : 11.073 79.855 1393 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.62 % Allowed : 17.97 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.26), residues: 996 helix: 2.76 (0.18), residues: 744 sheet: 0.05 (0.49), residues: 102 loop : -0.01 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 206 TYR 0.012 0.001 TYR D 67 PHE 0.005 0.001 PHE C 53 TRP 0.007 0.001 TRP E 277 HIS 0.003 0.001 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8754) covalent geometry : angle 0.59941 (11826) SS BOND : bond 0.00074 ( 18) SS BOND : angle 0.66440 ( 36) hydrogen bonds : bond 0.04201 ( 635) hydrogen bonds : angle 3.51531 ( 1869) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 273 ASN cc_start: 0.8237 (t0) cc_final: 0.7589 (t0) REVERT: B 273 ASN cc_start: 0.8398 (t0) cc_final: 0.7720 (t0) REVERT: F 273 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.7823 (t0) REVERT: C 273 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.7790 (t0) REVERT: D 269 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8294 (mt) REVERT: D 273 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7553 (t0) REVERT: E 233 ARG cc_start: 0.8101 (mmm-85) cc_final: 0.7829 (mmm-85) REVERT: E 273 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.7724 (t0) outliers start: 15 outliers final: 3 residues processed: 181 average time/residue: 1.1841 time to fit residues: 227.5190 Evaluate side-chains 180 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 273 ASN Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain E residue 273 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN D 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.078644 restraints weight = 30544.522| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 1.83 r_work: 0.2672 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8772 Z= 0.187 Angle : 0.624 11.001 11862 Z= 0.336 Chirality : 0.100 1.393 1338 Planarity : 0.003 0.028 1422 Dihedral : 9.863 59.656 1393 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.73 % Allowed : 17.86 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.26), residues: 996 helix: 2.64 (0.18), residues: 744 sheet: 0.06 (0.48), residues: 102 loop : -0.06 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 206 TYR 0.014 0.002 TYR E 67 PHE 0.006 0.001 PHE D 213 TRP 0.007 0.001 TRP B 277 HIS 0.004 0.001 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 8754) covalent geometry : angle 0.62375 (11826) SS BOND : bond 0.00112 ( 18) SS BOND : angle 0.78560 ( 36) hydrogen bonds : bond 0.04702 ( 635) hydrogen bonds : angle 3.59325 ( 1869) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 273 ASN cc_start: 0.8271 (t0) cc_final: 0.7588 (t0) REVERT: B 269 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8430 (mt) REVERT: B 273 ASN cc_start: 0.8395 (t0) cc_final: 0.7715 (t0) REVERT: F 52 MET cc_start: 0.9401 (mmt) cc_final: 0.8892 (mmt) REVERT: F 273 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.7836 (t0) REVERT: C 52 MET cc_start: 0.9385 (mmt) cc_final: 0.8865 (mmt) REVERT: C 273 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.7773 (t0) REVERT: D 269 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8353 (mt) REVERT: D 273 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7567 (t0) REVERT: E 233 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7870 (mmm-85) REVERT: E 273 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.8142 (m-40) outliers start: 16 outliers final: 6 residues processed: 183 average time/residue: 1.2766 time to fit residues: 247.8989 Evaluate side-chains 189 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 177 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 273 ASN Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 273 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 207 ASN F 207 ASN C 207 ASN D 207 ASN E 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.079063 restraints weight = 30539.523| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.87 r_work: 0.2693 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8772 Z= 0.139 Angle : 0.609 11.025 11862 Z= 0.325 Chirality : 0.100 1.397 1338 Planarity : 0.003 0.024 1422 Dihedral : 9.280 59.962 1393 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.52 % Allowed : 18.18 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.26), residues: 996 helix: 2.70 (0.18), residues: 744 sheet: 0.23 (0.49), residues: 102 loop : -0.00 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 206 TYR 0.013 0.002 TYR D 96 PHE 0.006 0.001 PHE D 53 TRP 0.007 0.001 TRP F 277 HIS 0.003 0.001 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8754) covalent geometry : angle 0.60912 (11826) SS BOND : bond 0.00079 ( 18) SS BOND : angle 0.68179 ( 36) hydrogen bonds : bond 0.04367 ( 635) hydrogen bonds : angle 3.51537 ( 1869) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASN cc_start: 0.8246 (t0) cc_final: 0.7608 (t0) REVERT: B 273 ASN cc_start: 0.8382 (t0) cc_final: 0.7673 (t0) REVERT: F 52 MET cc_start: 0.9397 (mmt) cc_final: 0.8914 (mmt) REVERT: F 273 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.7815 (t0) REVERT: F 278 ARG cc_start: 0.6921 (mmp80) cc_final: 0.6615 (mmp-170) REVERT: C 52 MET cc_start: 0.9378 (mmt) cc_final: 0.8882 (mmt) REVERT: C 273 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.7738 (t0) REVERT: D 269 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8351 (mt) REVERT: D 273 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7593 (t0) REVERT: E 233 ARG cc_start: 0.8175 (mmm-85) cc_final: 0.7859 (mmm-85) REVERT: E 273 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.8120 (m-40) outliers start: 14 outliers final: 5 residues processed: 178 average time/residue: 1.1026 time to fit residues: 208.2831 Evaluate side-chains 182 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain F residue 90 SER Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain C residue 273 ASN Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain E residue 273 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN D 207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.110904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.079444 restraints weight = 30584.492| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.82 r_work: 0.2687 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8772 Z= 0.151 Angle : 0.616 10.979 11862 Z= 0.328 Chirality : 0.100 1.385 1338 Planarity : 0.003 0.021 1422 Dihedral : 9.143 59.465 1393 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.73 % Allowed : 18.29 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.11 (0.26), residues: 996 helix: 2.71 (0.18), residues: 744 sheet: 0.24 (0.49), residues: 102 loop : -0.04 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 206 TYR 0.014 0.002 TYR A 96 PHE 0.006 0.001 PHE C 53 TRP 0.004 0.001 TRP F 277 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8754) covalent geometry : angle 0.61534 (11826) SS BOND : bond 0.00085 ( 18) SS BOND : angle 0.71336 ( 36) hydrogen bonds : bond 0.04403 ( 635) hydrogen bonds : angle 3.53514 ( 1869) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASN cc_start: 0.8252 (t0) cc_final: 0.7573 (t0) REVERT: B 269 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8415 (mt) REVERT: B 273 ASN cc_start: 0.8323 (t0) cc_final: 0.7620 (t0) REVERT: F 52 MET cc_start: 0.9402 (mmt) cc_final: 0.8905 (mmt) REVERT: F 273 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.7802 (t0) REVERT: F 278 ARG cc_start: 0.7019 (mmp80) cc_final: 0.6710 (mmp-170) REVERT: C 52 MET cc_start: 0.9383 (mmt) cc_final: 0.8876 (mmt) REVERT: C 273 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.7728 (t0) REVERT: D 269 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8351 (mt) REVERT: D 273 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7581 (t0) REVERT: E 233 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7833 (mmm-85) REVERT: E 273 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7607 (t0) outliers start: 16 outliers final: 6 residues processed: 180 average time/residue: 1.1701 time to fit residues: 224.0209 Evaluate side-chains 184 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 273 ASN Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 273 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 207 ASN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN D 207 ASN E 100 GLN E 207 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.080901 restraints weight = 31747.947| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.76 r_work: 0.2748 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8772 Z= 0.167 Angle : 0.617 10.993 11862 Z= 0.330 Chirality : 0.100 1.385 1338 Planarity : 0.003 0.019 1422 Dihedral : 9.146 57.087 1393 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.52 % Allowed : 18.40 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.26), residues: 996 helix: 2.69 (0.18), residues: 744 sheet: 0.22 (0.49), residues: 102 loop : -0.04 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.014 0.002 TYR A 96 PHE 0.007 0.001 PHE F 53 TRP 0.005 0.001 TRP A 277 HIS 0.003 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8754) covalent geometry : angle 0.61650 (11826) SS BOND : bond 0.00091 ( 18) SS BOND : angle 0.74191 ( 36) hydrogen bonds : bond 0.04540 ( 635) hydrogen bonds : angle 3.53390 ( 1869) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 ASN cc_start: 0.8258 (t0) cc_final: 0.7637 (t0) REVERT: B 273 ASN cc_start: 0.8347 (t0) cc_final: 0.7633 (t0) REVERT: F 273 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.7821 (t0) REVERT: F 278 ARG cc_start: 0.7072 (mmp80) cc_final: 0.6830 (mmp80) REVERT: C 273 ASN cc_start: 0.8366 (t0) cc_final: 0.7768 (t0) REVERT: D 269 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8471 (mt) REVERT: D 273 ASN cc_start: 0.8215 (t0) cc_final: 0.7596 (t0) REVERT: E 233 ARG cc_start: 0.8182 (mmm-85) cc_final: 0.7857 (mmm-85) REVERT: E 273 ASN cc_start: 0.8326 (OUTLIER) cc_final: 0.7606 (t0) outliers start: 14 outliers final: 6 residues processed: 181 average time/residue: 1.1390 time to fit residues: 218.9414 Evaluate side-chains 183 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain F residue 273 ASN Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 273 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN D 207 ASN E 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.081593 restraints weight = 31686.204| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.76 r_work: 0.2796 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8772 Z= 0.139 Angle : 0.616 10.959 11862 Z= 0.327 Chirality : 0.100 1.376 1338 Planarity : 0.003 0.019 1422 Dihedral : 9.071 57.171 1393 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.30 % Allowed : 18.94 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.26), residues: 996 helix: 2.73 (0.18), residues: 744 sheet: 0.28 (0.49), residues: 102 loop : -0.02 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 206 TYR 0.015 0.002 TYR A 96 PHE 0.006 0.001 PHE C 53 TRP 0.003 0.001 TRP A 277 HIS 0.003 0.001 HIS F 99 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8754) covalent geometry : angle 0.61562 (11826) SS BOND : bond 0.00084 ( 18) SS BOND : angle 0.70697 ( 36) hydrogen bonds : bond 0.04344 ( 635) hydrogen bonds : angle 3.51673 ( 1869) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1992 Ramachandran restraints generated. 996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Residue THR 20 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 ASN cc_start: 0.8278 (t0) cc_final: 0.7634 (t0) REVERT: A 278 ARG cc_start: 0.7139 (mmp80) cc_final: 0.6839 (mmp80) REVERT: B 273 ASN cc_start: 0.8350 (t0) cc_final: 0.7658 (t0) REVERT: F 273 ASN cc_start: 0.8421 (t0) cc_final: 0.7841 (t0) REVERT: F 278 ARG cc_start: 0.7072 (mmp80) cc_final: 0.6834 (mmp80) REVERT: C 273 ASN cc_start: 0.8373 (t0) cc_final: 0.7756 (t0) REVERT: D 269 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8501 (mt) REVERT: D 273 ASN cc_start: 0.8251 (t0) cc_final: 0.7598 (t0) REVERT: E 233 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7849 (mmm-85) REVERT: E 273 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.7592 (t0) outliers start: 12 outliers final: 5 residues processed: 180 average time/residue: 1.1087 time to fit residues: 212.2937 Evaluate side-chains 180 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 173 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 273 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 207 ASN ** F 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN D 207 ASN E 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.080630 restraints weight = 31769.393| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.78 r_work: 0.2749 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8772 Z= 0.172 Angle : 0.626 10.976 11862 Z= 0.333 Chirality : 0.100 1.383 1338 Planarity : 0.003 0.020 1422 Dihedral : 9.199 54.901 1393 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.08 % Allowed : 19.05 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.26), residues: 996 helix: 2.68 (0.18), residues: 744 sheet: 0.22 (0.49), residues: 102 loop : -0.04 (0.51), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 206 TYR 0.015 0.002 TYR A 96 PHE 0.007 0.001 PHE F 53 TRP 0.003 0.001 TRP C 79 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8754) covalent geometry : angle 0.62524 (11826) SS BOND : bond 0.00095 ( 18) SS BOND : angle 0.73521 ( 36) hydrogen bonds : bond 0.04576 ( 635) hydrogen bonds : angle 3.54595 ( 1869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5916.44 seconds wall clock time: 100 minutes 35.07 seconds (6035.07 seconds total)