Starting phenix.real_space_refine on Thu Feb 5 16:48:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ipo_60779/02_2026/9ipo_60779_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ipo_60779/02_2026/9ipo_60779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ipo_60779/02_2026/9ipo_60779_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ipo_60779/02_2026/9ipo_60779_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ipo_60779/02_2026/9ipo_60779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ipo_60779/02_2026/9ipo_60779.map" } resolution = 2.41 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 12 5.49 5 S 78 5.16 5 C 6108 2.51 5 N 1338 2.21 5 O 1494 1.98 5 H 8286 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s 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: 17316 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2753 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain breaks: 1 Chain: "B" Number of atoms: 2753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2753 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain breaks: 1 Chain: "F" Number of atoms: 2753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2753 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain breaks: 1 Chain: "C" Number of atoms: 2753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2753 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain breaks: 1 Chain: "D" Number of atoms: 2753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2753 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain breaks: 1 Chain: "E" Number of atoms: 2753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2753 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 163} Chain breaks: 1 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'C14': 4, 'MC3': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 133 Unusual residues: {'C14': 3, 'MC3': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'C14': 2, 'MC3': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 133 Unusual residues: {'C14': 3, 'MC3': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 133 Unusual residues: {'C14': 3, 'MC3': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 133 Unusual residues: {'C14': 3, 'MC3': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.43, per 1000 atoms: 0.14 Number of scatterers: 17316 At special positions: 0 Unit cell: (104.49, 96.39, 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 12 15.00 O 1494 8.00 N 1338 7.00 C 6108 6.00 H 8286 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: 1.12 Conformation dependent library (CDL) restraints added in 399.4 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 72.9% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 20 through 46 removed outlier: 5.446A pdb=" N GLU A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 4.948A 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 275 Processing helix chain 'B' and resid 20 through 46 removed outlier: 5.470A pdb=" N GLU B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.946A 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 275 Processing helix chain 'F' and resid 20 through 46 removed outlier: 5.455A pdb=" N GLU F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 4.977A 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: 5.457A pdb=" N GLU C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 4.976A 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: 5.452A pdb=" N GLU D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 4.947A 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 275 Processing helix chain 'E' and resid 20 through 46 removed outlier: 5.473A pdb=" N GLU E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 4.946A 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 275 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 55 630 hydrogen bonds defined for protein. 1854 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 1.50 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: 8268 1.03 - 1.23: 82 1.23 - 1.42: 3650 1.42 - 1.61: 5364 1.61 - 1.81: 126 Bond restraints: 17490 Sorted by residual: bond pdb=" C11 MC3 D 402 " pdb=" O3 MC3 D 402 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C11 MC3 A 402 " pdb=" O3 MC3 A 402 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C11 MC3 B 402 " pdb=" O3 MC3 B 402 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C11 MC3 C 402 " pdb=" O3 MC3 C 402 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C11 MC3 E 403 " pdb=" O3 MC3 E 403 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 17485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.04: 30864 7.04 - 14.09: 60 14.09 - 21.13: 12 21.13 - 28.18: 18 28.18 - 35.22: 36 Bond angle restraints: 30990 Sorted by residual: angle pdb=" C LYS E 279 " pdb=" CA LYS E 279 " pdb=" HA LYS E 279 " ideal model delta sigma weight residual 109.00 73.78 35.22 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C LYS A 279 " pdb=" CA LYS A 279 " pdb=" HA LYS A 279 " ideal model delta sigma weight residual 109.00 73.81 35.19 3.00e+00 1.11e-01 1.38e+02 angle pdb=" C LYS B 279 " pdb=" CA LYS B 279 " pdb=" HA LYS B 279 " ideal model delta sigma weight residual 109.00 73.82 35.18 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C LYS D 279 " pdb=" CA LYS D 279 " pdb=" HA LYS D 279 " ideal model delta sigma weight residual 109.00 73.84 35.16 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C LYS C 279 " pdb=" CA LYS C 279 " pdb=" HA LYS C 279 " ideal model delta sigma weight residual 109.00 73.86 35.14 3.00e+00 1.11e-01 1.37e+02 ... (remaining 30985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.59: 7834 25.59 - 51.17: 642 51.17 - 76.76: 99 76.76 - 102.35: 11 102.35 - 127.93: 12 Dihedral angle restraints: 8598 sinusoidal: 4854 harmonic: 3744 Sorted by residual: dihedral pdb=" C ILE C 280 " pdb=" N ILE C 280 " pdb=" CA ILE C 280 " pdb=" CB ILE C 280 " ideal model delta harmonic sigma weight residual -122.00 -132.62 10.62 0 2.50e+00 1.60e-01 1.80e+01 dihedral pdb=" C ILE B 280 " pdb=" N ILE B 280 " pdb=" CA ILE B 280 " pdb=" CB ILE B 280 " ideal model delta harmonic sigma weight residual -122.00 -132.57 10.57 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" C ILE A 280 " pdb=" N ILE A 280 " pdb=" CA ILE A 280 " pdb=" CB ILE A 280 " ideal model delta harmonic sigma weight residual -122.00 -132.54 10.54 0 2.50e+00 1.60e-01 1.78e+01 ... (remaining 8595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.284: 1326 0.284 - 0.569: 12 0.569 - 0.853: 0 0.853 - 1.138: 0 1.138 - 1.422: 6 Chirality restraints: 1344 Sorted by residual: 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 1.13 1.42 2.00e-01 2.50e+01 5.05e+01 chirality pdb=" CB THR D 20 " pdb=" CA THR D 20 " pdb=" OG1 THR D 20 " pdb=" CG2 THR D 20 " both_signs ideal model delta sigma weight residual False 2.55 1.13 1.42 2.00e-01 2.50e+01 5.02e+01 chirality pdb=" CB THR B 20 " pdb=" CA THR B 20 " pdb=" OG1 THR B 20 " pdb=" CG2 THR B 20 " both_signs ideal model delta sigma weight residual False 2.55 1.14 1.41 2.00e-01 2.50e+01 5.00e+01 ... (remaining 1341 not shown) Planarity restraints: 2406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 278 " 0.270 9.50e-02 1.11e+02 9.06e-02 1.12e+01 pdb=" NE ARG E 278 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG E 278 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG E 278 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG E 278 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG E 278 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG E 278 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG E 278 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG E 278 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " 0.268 9.50e-02 1.11e+02 9.02e-02 1.11e+01 pdb=" NE ARG A 278 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 278 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 278 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 278 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 278 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 278 " 0.269 9.50e-02 1.11e+02 9.03e-02 1.11e+01 pdb=" NE ARG F 278 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG F 278 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG F 278 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG F 278 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG F 278 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG F 278 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG F 278 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG F 278 " -0.001 2.00e-02 2.50e+03 ... (remaining 2403 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1279 2.21 - 2.81: 34341 2.81 - 3.41: 46466 3.41 - 4.00: 61617 4.00 - 4.60: 93326 Nonbonded interactions: 237029 Sorted by model distance: nonbonded pdb=" HA LYS F 279 " pdb=" HB2 LYS F 279 " model vdw 1.616 1.952 nonbonded pdb=" HA LYS C 279 " pdb=" HB2 LYS C 279 " model vdw 1.616 1.952 nonbonded pdb=" HA LYS B 279 " pdb=" HB2 LYS B 279 " model vdw 1.617 1.952 nonbonded pdb=" HA LYS E 279 " pdb=" HB2 LYS E 279 " model vdw 1.617 1.952 nonbonded pdb=" HA LYS A 279 " pdb=" HB2 LYS A 279 " model vdw 1.618 1.952 ... (remaining 237024 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 280 or resid 402 or resid 404)) selection = (chain 'B' and (resid 19 through 280 or resid 402 or resid 404)) selection = (chain 'C' and (resid 19 through 280 or resid 402 or resid 404)) selection = (chain 'D' and (resid 19 through 280 or resid 402 or resid 404)) selection = (chain 'E' and (resid 19 through 280 or resid 402 or resid 404)) selection = (chain 'F' and (resid 19 through 280 or resid 402 or resid 404)) } 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: 1.230 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: 0.080 Extract box with map and model: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.670 Find NCS groups from input model: 0.320 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:8.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 0.008 0.073 9222 Z= 0.377 Angle : 1.348 17.070 12348 Z= 0.557 Chirality : 0.108 1.422 1344 Planarity : 0.008 0.121 1434 Dihedral : 20.214 127.933 3636 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.11 % Allowed : 23.05 % Favored : 76.84 % 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: -0.09 (0.24), residues: 996 helix: 0.36 (0.17), residues: 732 sheet: -0.76 (0.51), residues: 102 loop : -0.93 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG D 278 TYR 0.014 0.002 TYR A 243 PHE 0.008 0.001 PHE B 198 TRP 0.004 0.001 TRP F 79 HIS 0.009 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00820 ( 9204) covalent geometry : angle 1.34951 (12312) SS BOND : bond 0.00087 ( 18) SS BOND : angle 0.76656 ( 36) hydrogen bonds : bond 0.09873 ( 630) hydrogen bonds : angle 4.71206 ( 1854) *********************** 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 **************************** Evaluate side-chains 171 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 21 MET cc_start: 0.8345 (tpt) cc_final: 0.8062 (mmp) outliers start: 1 outliers final: 1 residues processed: 171 average time/residue: 1.0194 time to fit residues: 185.8132 Evaluate side-chains 162 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.075957 restraints weight = 34978.806| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.86 r_work: 0.2701 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.0595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9222 Z= 0.155 Angle : 0.681 11.283 12348 Z= 0.358 Chirality : 0.107 1.413 1344 Planarity : 0.004 0.046 1434 Dihedral : 16.564 130.150 1783 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 22.51 % Favored : 77.49 % 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: 1.73 (0.26), residues: 996 helix: 1.74 (0.18), residues: 732 sheet: -0.49 (0.53), residues: 102 loop : -0.31 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 278 TYR 0.010 0.001 TYR D 96 PHE 0.006 0.001 PHE F 198 TRP 0.002 0.000 TRP F 79 HIS 0.006 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9204) covalent geometry : angle 0.68118 (12312) SS BOND : bond 0.00125 ( 18) SS BOND : angle 0.72476 ( 36) hydrogen bonds : bond 0.05135 ( 630) hydrogen bonds : angle 4.06648 ( 1854) *********************** 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 **************************** Evaluate side-chains 167 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: F 230 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8578 (mm-30) REVERT: C 230 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8595 (mm-30) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 1.0674 time to fit residues: 190.4496 Evaluate side-chains 162 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 81 optimal weight: 0.0970 chunk 90 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN E 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.077408 restraints weight = 34863.970| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.88 r_work: 0.2726 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9222 Z= 0.120 Angle : 0.653 11.363 12348 Z= 0.343 Chirality : 0.107 1.415 1344 Planarity : 0.004 0.047 1434 Dihedral : 15.816 127.550 1782 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.32 % Allowed : 21.97 % Favored : 77.71 % Cbeta Deviations : 0.21 % 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: 2.38 (0.26), residues: 996 helix: 2.19 (0.18), residues: 738 sheet: -0.43 (0.53), residues: 102 loop : 0.14 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 278 TYR 0.011 0.001 TYR D 96 PHE 0.005 0.001 PHE F 256 TRP 0.004 0.001 TRP A 277 HIS 0.006 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9204) covalent geometry : angle 0.65301 (12312) SS BOND : bond 0.00108 ( 18) SS BOND : angle 0.60518 ( 36) hydrogen bonds : bond 0.04527 ( 630) hydrogen bonds : angle 3.92261 ( 1854) *********************** 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 **************************** Evaluate side-chains 176 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 173 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: E 25 ILE cc_start: 0.8899 (tp) cc_final: 0.8625 (tp) outliers start: 3 outliers final: 0 residues processed: 176 average time/residue: 1.1080 time to fit residues: 207.7504 Evaluate side-chains 166 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 0.0870 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.103513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.076226 restraints weight = 35082.970| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.87 r_work: 0.2708 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9222 Z= 0.163 Angle : 0.667 11.328 12348 Z= 0.351 Chirality : 0.107 1.415 1344 Planarity : 0.003 0.037 1434 Dihedral : 15.608 126.057 1782 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.43 % Allowed : 22.73 % Favored : 76.84 % Cbeta Deviations : 0.21 % 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: 2.65 (0.26), residues: 996 helix: 2.41 (0.18), residues: 738 sheet: -0.49 (0.52), residues: 102 loop : 0.23 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 278 TYR 0.011 0.001 TYR D 96 PHE 0.006 0.001 PHE C 198 TRP 0.003 0.001 TRP D 277 HIS 0.006 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9204) covalent geometry : angle 0.66724 (12312) SS BOND : bond 0.00091 ( 18) SS BOND : angle 0.68978 ( 36) hydrogen bonds : bond 0.04606 ( 630) hydrogen bonds : angle 3.93945 ( 1854) *********************** 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 **************************** Evaluate side-chains 171 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 167 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: B 25 ILE cc_start: 0.8897 (tp) cc_final: 0.8614 (tp) REVERT: E 25 ILE cc_start: 0.8905 (tp) cc_final: 0.8637 (tp) outliers start: 4 outliers final: 3 residues processed: 168 average time/residue: 1.0640 time to fit residues: 191.2651 Evaluate side-chains 170 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 232 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 44 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN B 232 ASN E 207 ASN E 232 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.104061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.076890 restraints weight = 34972.494| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.87 r_work: 0.2719 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9222 Z= 0.139 Angle : 0.660 11.361 12348 Z= 0.347 Chirality : 0.107 1.419 1344 Planarity : 0.004 0.045 1434 Dihedral : 15.300 124.199 1782 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.54 % Allowed : 22.19 % Favored : 77.27 % 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: 2.84 (0.26), residues: 996 helix: 2.57 (0.18), residues: 738 sheet: -0.49 (0.53), residues: 102 loop : 0.18 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 278 TYR 0.012 0.001 TYR B 96 PHE 0.006 0.001 PHE C 198 TRP 0.004 0.001 TRP D 277 HIS 0.008 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9204) covalent geometry : angle 0.66013 (12312) SS BOND : bond 0.00081 ( 18) SS BOND : angle 0.64122 ( 36) hydrogen bonds : bond 0.04420 ( 630) hydrogen bonds : angle 3.87841 ( 1854) *********************** 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 **************************** Evaluate side-chains 173 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: B 25 ILE cc_start: 0.8908 (tp) cc_final: 0.8630 (tp) REVERT: F 69 ARG cc_start: 0.8697 (tpt170) cc_final: 0.8473 (tpt170) REVERT: E 25 ILE cc_start: 0.8899 (tp) cc_final: 0.8617 (tp) outliers start: 5 outliers final: 2 residues processed: 171 average time/residue: 1.0025 time to fit residues: 184.1947 Evaluate side-chains 168 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain E residue 232 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 63 optimal weight: 0.0670 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.078001 restraints weight = 34878.731| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.87 r_work: 0.2738 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9222 Z= 0.116 Angle : 0.657 11.362 12348 Z= 0.345 Chirality : 0.107 1.417 1344 Planarity : 0.006 0.084 1434 Dihedral : 14.931 122.767 1782 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.54 % Allowed : 21.86 % Favored : 77.60 % Cbeta Deviations : 0.21 % 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: 2.94 (0.26), residues: 996 helix: 2.64 (0.18), residues: 738 sheet: -0.34 (0.54), residues: 102 loop : 0.12 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 278 TYR 0.012 0.001 TYR B 96 PHE 0.004 0.001 PHE C 198 TRP 0.004 0.001 TRP A 277 HIS 0.007 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9204) covalent geometry : angle 0.65713 (12312) SS BOND : bond 0.00081 ( 18) SS BOND : angle 0.58731 ( 36) hydrogen bonds : bond 0.04107 ( 630) hydrogen bonds : angle 3.85918 ( 1854) *********************** 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 **************************** Evaluate side-chains 176 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 171 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: B 25 ILE cc_start: 0.8885 (tp) cc_final: 0.8597 (tp) REVERT: F 238 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8891 (mppt) REVERT: C 238 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8904 (mppt) REVERT: D 21 MET cc_start: 0.8416 (tpt) cc_final: 0.8208 (mmp) REVERT: E 25 ILE cc_start: 0.8848 (tp) cc_final: 0.8570 (tp) outliers start: 5 outliers final: 0 residues processed: 171 average time/residue: 1.0160 time to fit residues: 186.6247 Evaluate side-chains 171 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 169 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain C residue 238 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN B 232 ASN E 207 ASN E 232 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.103925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.076741 restraints weight = 35190.080| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.86 r_work: 0.2709 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9222 Z= 0.166 Angle : 0.680 11.308 12348 Z= 0.355 Chirality : 0.107 1.411 1344 Planarity : 0.007 0.096 1434 Dihedral : 14.873 120.805 1782 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.87 % Allowed : 22.19 % Favored : 76.95 % 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: 3.02 (0.26), residues: 996 helix: 2.73 (0.18), residues: 738 sheet: -0.52 (0.52), residues: 102 loop : 0.16 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 278 TYR 0.014 0.001 TYR B 96 PHE 0.006 0.001 PHE C 198 TRP 0.006 0.001 TRP D 277 HIS 0.007 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9204) covalent geometry : angle 0.68043 (12312) SS BOND : bond 0.00096 ( 18) SS BOND : angle 0.66996 ( 36) hydrogen bonds : bond 0.04394 ( 630) hydrogen bonds : angle 3.87920 ( 1854) *********************** 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 **************************** Evaluate side-chains 174 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 166 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ILE cc_start: 0.8873 (tp) cc_final: 0.8590 (tp) REVERT: B 238 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.9025 (mtpt) REVERT: F 238 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8957 (mppt) REVERT: C 238 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8960 (mppt) REVERT: D 21 MET cc_start: 0.8441 (tpt) cc_final: 0.8139 (mmp) REVERT: E 25 ILE cc_start: 0.8826 (tp) cc_final: 0.8549 (tp) REVERT: E 238 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.9024 (mtpt) outliers start: 8 outliers final: 2 residues processed: 167 average time/residue: 1.0824 time to fit residues: 193.6630 Evaluate side-chains 170 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 164 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain E residue 232 ASN Chi-restraints excluded: chain E residue 238 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 ASN E 232 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.103999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.076733 restraints weight = 35251.627| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.87 r_work: 0.2709 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9222 Z= 0.161 Angle : 0.690 11.330 12348 Z= 0.360 Chirality : 0.107 1.412 1344 Planarity : 0.006 0.110 1434 Dihedral : 14.802 119.259 1782 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.76 % Allowed : 22.51 % Favored : 76.73 % 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: 3.00 (0.26), residues: 996 helix: 2.73 (0.18), residues: 738 sheet: -0.51 (0.52), residues: 102 loop : 0.06 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 278 TYR 0.014 0.001 TYR B 96 PHE 0.005 0.001 PHE B 213 TRP 0.005 0.001 TRP A 277 HIS 0.007 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9204) covalent geometry : angle 0.69013 (12312) SS BOND : bond 0.00099 ( 18) SS BOND : angle 0.72025 ( 36) hydrogen bonds : bond 0.04390 ( 630) hydrogen bonds : angle 3.89563 ( 1854) *********************** 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 **************************** Evaluate side-chains 171 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ILE cc_start: 0.8870 (tp) cc_final: 0.8586 (tp) REVERT: B 238 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8970 (mtpt) REVERT: D 21 MET cc_start: 0.8482 (tpt) cc_final: 0.8182 (mmp) REVERT: E 238 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8968 (mtpt) outliers start: 7 outliers final: 1 residues processed: 165 average time/residue: 1.0073 time to fit residues: 178.1036 Evaluate side-chains 166 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 163 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain E residue 238 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN B 232 ASN E 207 ASN E 232 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.105271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.078075 restraints weight = 35084.519| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.87 r_work: 0.2733 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9222 Z= 0.120 Angle : 0.666 11.372 12348 Z= 0.346 Chirality : 0.107 1.418 1344 Planarity : 0.004 0.137 1434 Dihedral : 14.294 115.861 1782 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.52 % Allowed : 21.65 % Favored : 76.84 % 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: 2.78 (0.18), residues: 738 sheet: -0.35 (0.53), residues: 102 loop : 0.04 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 278 TYR 0.015 0.001 TYR B 96 PHE 0.004 0.001 PHE C 198 TRP 0.008 0.001 TRP E 277 HIS 0.006 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9204) covalent geometry : angle 0.66626 (12312) SS BOND : bond 0.00098 ( 18) SS BOND : angle 0.55476 ( 36) hydrogen bonds : bond 0.04008 ( 630) hydrogen bonds : angle 3.81665 ( 1854) *********************** 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 **************************** Evaluate side-chains 175 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 238 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8966 (mtpt) REVERT: F 69 ARG cc_start: 0.8659 (tpt170) cc_final: 0.8399 (tpt170) REVERT: F 238 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8937 (mppt) REVERT: C 238 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8966 (mppt) REVERT: D 21 MET cc_start: 0.8464 (tpt) cc_final: 0.8221 (mmp) REVERT: E 238 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8954 (mtpt) outliers start: 14 outliers final: 2 residues processed: 164 average time/residue: 0.9793 time to fit residues: 172.4306 Evaluate side-chains 166 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain E residue 238 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 ASN D 207 ASN E 232 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.077721 restraints weight = 34847.637| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.86 r_work: 0.2727 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9222 Z= 0.135 Angle : 0.675 11.301 12348 Z= 0.351 Chirality : 0.107 1.403 1344 Planarity : 0.006 0.129 1434 Dihedral : 14.145 113.009 1782 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.76 % Allowed : 22.40 % Favored : 76.84 % 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: 2.79 (0.18), residues: 738 sheet: -0.34 (0.53), residues: 102 loop : 0.05 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 278 TYR 0.014 0.001 TYR B 96 PHE 0.004 0.001 PHE A 213 TRP 0.005 0.001 TRP C 277 HIS 0.006 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9204) covalent geometry : angle 0.67530 (12312) SS BOND : bond 0.00079 ( 18) SS BOND : angle 0.61731 ( 36) hydrogen bonds : bond 0.04063 ( 630) hydrogen bonds : angle 3.86578 ( 1854) ********************** 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 **************************** Evaluate side-chains 166 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 238 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.9004 (mtpt) REVERT: F 69 ARG cc_start: 0.8656 (tpt170) cc_final: 0.8398 (tpt170) REVERT: F 238 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8919 (mppt) REVERT: C 238 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8952 (mppt) REVERT: D 21 MET cc_start: 0.8470 (tpt) cc_final: 0.8247 (mmp) REVERT: E 238 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8997 (mtpt) outliers start: 7 outliers final: 2 residues processed: 159 average time/residue: 0.9892 time to fit residues: 168.5621 Evaluate side-chains 163 residues out of total 924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain E residue 238 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN E 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.078625 restraints weight = 35106.464| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.85 r_work: 0.2739 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9222 Z= 0.117 Angle : 0.656 11.369 12348 Z= 0.340 Chirality : 0.107 1.423 1344 Planarity : 0.004 0.100 1434 Dihedral : 13.794 108.034 1782 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.87 % Allowed : 22.08 % Favored : 77.06 % 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: 3.20 (0.26), residues: 996 helix: 2.85 (0.18), residues: 738 sheet: -0.24 (0.53), residues: 102 loop : 0.10 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG E 278 TYR 0.014 0.001 TYR B 96 PHE 0.003 0.001 PHE F 33 TRP 0.004 0.001 TRP E 277 HIS 0.005 0.001 HIS E 99 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9204) covalent geometry : angle 0.65645 (12312) SS BOND : bond 0.00077 ( 18) SS BOND : angle 0.57937 ( 36) hydrogen bonds : bond 0.03916 ( 630) hydrogen bonds : angle 3.82262 ( 1854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6092.50 seconds wall clock time: 103 minutes 38.80 seconds (6218.80 seconds total)