Starting phenix.real_space_refine on Sun Aug 24 04:03:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8izy_35877/08_2025/8izy_35877_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8izy_35877/08_2025/8izy_35877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8izy_35877/08_2025/8izy_35877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8izy_35877/08_2025/8izy_35877.map" model { file = "/net/cci-nas-00/data/ceres_data/8izy_35877/08_2025/8izy_35877_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8izy_35877/08_2025/8izy_35877_neut_trim.cif" } resolution = 2.5 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= -0.000 sd= 0.004 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 S 36 5.16 5 C 5616 2.51 5 N 1400 2.21 5 O 1356 1.98 5 F 8 1.80 5 H 8360 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16776 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4144 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 4167 Chain: "B" Number of atoms: 4144 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 4167 Chain: "C" Number of atoms: 4144 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 4167 Chain: "D" Number of atoms: 4144 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 251, 4128 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 4, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 4167 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {'9MF': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'9MF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'9MF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'9MF': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AVAL A 132 " occ=0.50 ... (30 atoms not shown) pdb="HG23BVAL A 132 " occ=0.50 residue: pdb=" N AVAL B 132 " occ=0.50 ... (30 atoms not shown) pdb="HG23BVAL B 132 " occ=0.50 residue: pdb=" N AVAL C 132 " occ=0.50 ... (30 atoms not shown) pdb="HG23BVAL C 132 " occ=0.50 residue: pdb=" N AVAL D 132 " occ=0.50 ... (30 atoms not shown) pdb="HG23BVAL D 132 " occ=0.50 Time building chain proxies: 5.45, per 1000 atoms: 0.32 Number of scatterers: 16776 At special positions: 0 Unit cell: (128.778, 128.778, 77.064, 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 36 16.00 F 8 9.00 O 1356 8.00 N 1400 7.00 C 5616 6.00 H 8360 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.40 Conformation dependent library (CDL) restraints added in 609.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1864 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 86.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 71 through 86 Processing helix chain 'A' and resid 92 through 114 removed outlier: 3.783A pdb=" N HIS A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 removed outlier: 4.240A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.663A pdb=" N ALA A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 196 through 211 Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 228 through 254 Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 287 through 330 removed outlier: 3.916A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'B' and resid 71 through 86 Processing helix chain 'B' and resid 92 through 114 removed outlier: 3.779A pdb=" N HIS B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 removed outlier: 4.170A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 155 through 164 removed outlier: 3.666A pdb=" N ALA B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 184 Processing helix chain 'B' and resid 196 through 211 Processing helix chain 'B' and resid 215 through 228 Processing helix chain 'B' and resid 228 through 254 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 287 through 330 removed outlier: 3.920A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 92 through 114 removed outlier: 3.783A pdb=" N HIS C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 removed outlier: 4.238A pdb=" N ILE C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 151 No H-bonds generated for 'chain 'C' and resid 149 through 151' Processing helix chain 'C' and resid 155 through 164 removed outlier: 3.667A pdb=" N ALA C 164 " --> pdb=" O ARG C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 184 Processing helix chain 'C' and resid 196 through 211 Processing helix chain 'C' and resid 215 through 228 Processing helix chain 'C' and resid 228 through 254 Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 287 through 330 removed outlier: 3.922A pdb=" N THR C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Proline residue: C 308 - end of helix Processing helix chain 'D' and resid 71 through 86 Processing helix chain 'D' and resid 92 through 114 removed outlier: 3.779A pdb=" N HIS D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 removed outlier: 4.237A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 151 No H-bonds generated for 'chain 'D' and resid 149 through 151' Processing helix chain 'D' and resid 155 through 164 removed outlier: 3.733A pdb=" N ALA D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 184 Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 215 through 228 Processing helix chain 'D' and resid 228 through 254 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 287 through 330 removed outlier: 3.920A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix 668 hydrogen bonds defined for protein. 2008 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: 3.36 Time building geometry restraints manager: 1.91 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: 8336 1.03 - 1.23: 40 1.23 - 1.42: 3860 1.42 - 1.61: 4728 1.61 - 1.81: 48 Bond restraints: 17012 Sorted by residual: bond pdb=" C09 9MF D 801 " pdb=" N08 9MF D 801 " ideal model delta sigma weight residual 1.352 1.452 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C09 9MF C 801 " pdb=" N08 9MF C 801 " ideal model delta sigma weight residual 1.352 1.451 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C09 9MF A 803 " pdb=" N08 9MF A 803 " ideal model delta sigma weight residual 1.352 1.451 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C09 9MF B 801 " pdb=" N08 9MF B 801 " ideal model delta sigma weight residual 1.352 1.451 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C09 9MF A 801 " pdb=" N08 9MF A 801 " ideal model delta sigma weight residual 1.352 1.451 -0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 17007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 30302 2.02 - 4.04: 177 4.04 - 6.06: 29 6.06 - 8.08: 8 8.08 - 10.10: 8 Bond angle restraints: 30524 Sorted by residual: angle pdb=" N08 9MF A 801 " pdb=" C09 9MF A 801 " pdb=" O11 9MF A 801 " ideal model delta sigma weight residual 110.34 120.44 -10.10 3.00e+00 1.11e-01 1.13e+01 angle pdb=" N ARG B 213 " pdb=" CA ARG B 213 " pdb=" CB ARG B 213 " ideal model delta sigma weight residual 114.17 110.33 3.84 1.14e+00 7.69e-01 1.13e+01 angle pdb=" N08 9MF C 802 " pdb=" C09 9MF C 802 " pdb=" O11 9MF C 802 " ideal model delta sigma weight residual 110.34 120.41 -10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" N08 9MF B 802 " pdb=" C09 9MF B 802 " pdb=" O11 9MF B 802 " ideal model delta sigma weight residual 110.34 120.37 -10.03 3.00e+00 1.11e-01 1.12e+01 angle pdb=" N ARG A 213 " pdb=" CA ARG A 213 " pdb=" CB ARG A 213 " ideal model delta sigma weight residual 114.17 110.36 3.81 1.14e+00 7.69e-01 1.11e+01 ... (remaining 30519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6885 17.96 - 35.91: 671 35.91 - 53.87: 250 53.87 - 71.83: 82 71.83 - 89.79: 12 Dihedral angle restraints: 7900 sinusoidal: 4120 harmonic: 3780 Sorted by residual: dihedral pdb=" CA ARG C 207 " pdb=" CB ARG C 207 " pdb=" CG ARG C 207 " pdb=" CD ARG C 207 " ideal model delta sinusoidal sigma weight residual 180.00 121.23 58.77 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG B 207 " pdb=" CB ARG B 207 " pdb=" CG ARG B 207 " pdb=" CD ARG B 207 " ideal model delta sinusoidal sigma weight residual 180.00 121.27 58.73 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA ARG C 89 " pdb=" CB ARG C 89 " pdb=" CG ARG C 89 " pdb=" CD ARG C 89 " ideal model delta sinusoidal sigma weight residual 180.00 122.13 57.87 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 7897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 816 0.025 - 0.049: 258 0.049 - 0.074: 116 0.074 - 0.099: 52 0.099 - 0.123: 18 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CB THR A 298 " pdb=" CA THR A 298 " pdb=" OG1 THR A 298 " pdb=" CG2 THR A 298 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CB THR D 298 " pdb=" CA THR D 298 " pdb=" OG1 THR D 298 " pdb=" CG2 THR D 298 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CB THR C 298 " pdb=" CA THR C 298 " pdb=" OG1 THR C 298 " pdb=" CG2 THR C 298 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 1257 not shown) Planarity restraints: 2408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 214 " -0.136 9.50e-02 1.11e+02 4.55e-02 2.47e+00 pdb=" NE ARG C 214 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG C 214 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 214 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 214 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 214 " 0.005 2.00e-02 2.50e+03 pdb="HH12 ARG C 214 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG C 214 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 214 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 214 " -0.135 9.50e-02 1.11e+02 4.51e-02 2.46e+00 pdb=" NE ARG D 214 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG D 214 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 214 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 214 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG D 214 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG D 214 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 214 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 214 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 214 " -0.135 9.50e-02 1.11e+02 4.51e-02 2.43e+00 pdb=" NE ARG B 214 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 214 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 214 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 214 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 214 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B 214 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 214 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 214 " -0.000 2.00e-02 2.50e+03 ... (remaining 2405 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 2262 2.26 - 2.84: 36660 2.84 - 3.43: 43923 3.43 - 4.01: 56962 4.01 - 4.60: 87682 Nonbonded interactions: 227489 Sorted by model distance: nonbonded pdb=" OE2 GLU D 254 " pdb=" H GLN D 286 " model vdw 1.671 2.450 nonbonded pdb=" OE2 GLU B 254 " pdb=" H GLN B 286 " model vdw 1.675 2.450 nonbonded pdb=" OE2 GLU A 254 " pdb=" H GLN A 286 " model vdw 1.676 2.450 nonbonded pdb=" OE2 GLU C 254 " pdb=" H GLN C 286 " model vdw 1.677 2.450 nonbonded pdb=" OD2 ASP C 212 " pdb=" HG1 THR C 217 " model vdw 1.718 2.450 ... (remaining 227484 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 70 through 131 or resid 133 through 801)) selection = (chain 'B' and (resid 70 through 131 or resid 133 through 801)) selection = (chain 'C' and (resid 70 through 131 or resid 133 through 801)) selection = (chain 'D' and (resid 70 through 131 or resid 133 through 801)) } 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=0.50 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: 0.830 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: 0.060 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 17.480 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 : 0.006 0.100 8652 Z= 0.285 Angle : 0.648 10.101 11720 Z= 0.310 Chirality : 0.034 0.123 1260 Planarity : 0.004 0.059 1420 Dihedral : 17.996 89.785 3020 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.71 % Allowed : 28.32 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.26), residues: 1000 helix: 2.30 (0.17), residues: 844 sheet: None (None), residues: 0 loop : -1.45 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 214 TYR 0.008 0.001 TYR D 74 PHE 0.009 0.001 PHE D 100 TRP 0.007 0.001 TRP D 269 HIS 0.002 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00580 ( 8652) covalent geometry : angle 0.64798 (11720) hydrogen bonds : bond 0.10332 ( 668) hydrogen bonds : angle 4.86329 ( 2008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.6919 (tptt) cc_final: 0.6700 (tptp) REVERT: A 214 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.7000 (mtp85) REVERT: A 324 HIS cc_start: 0.7696 (t70) cc_final: 0.7245 (t-90) REVERT: A 327 LYS cc_start: 0.7343 (tppt) cc_final: 0.6662 (tttp) REVERT: B 76 LYS cc_start: 0.6896 (tptt) cc_final: 0.6673 (tptp) REVERT: B 214 ARG cc_start: 0.7240 (ttm-80) cc_final: 0.7004 (mtp85) REVERT: B 324 HIS cc_start: 0.7650 (t70) cc_final: 0.7201 (t-90) REVERT: B 327 LYS cc_start: 0.7339 (tppt) cc_final: 0.6657 (tttp) REVERT: C 76 LYS cc_start: 0.6930 (tptt) cc_final: 0.6709 (tptp) REVERT: C 214 ARG cc_start: 0.7387 (ttm-80) cc_final: 0.7139 (mtp85) REVERT: C 324 HIS cc_start: 0.7711 (t70) cc_final: 0.7265 (t-90) REVERT: C 327 LYS cc_start: 0.7341 (tppt) cc_final: 0.6658 (tttp) REVERT: D 162 LYS cc_start: 0.6336 (pptt) cc_final: 0.5643 (mtmm) REVERT: D 214 ARG cc_start: 0.7393 (ttm-80) cc_final: 0.7143 (mtp85) REVERT: D 324 HIS cc_start: 0.7677 (t70) cc_final: 0.7237 (t-90) outliers start: 6 outliers final: 4 residues processed: 153 average time/residue: 1.1610 time to fit residues: 188.8809 Evaluate side-chains 136 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain D residue 135 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.177928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.126242 restraints weight = 76710.225| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.26 r_work: 0.3408 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8652 Z= 0.132 Angle : 0.506 5.770 11720 Z= 0.268 Chirality : 0.034 0.118 1260 Planarity : 0.004 0.047 1420 Dihedral : 9.721 79.014 1208 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.37 % Allowed : 28.55 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.85 (0.26), residues: 1000 helix: 2.39 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.38 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 214 TYR 0.008 0.001 TYR D 74 PHE 0.012 0.001 PHE A 297 TRP 0.007 0.001 TRP A 269 HIS 0.003 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8652) covalent geometry : angle 0.50640 (11720) hydrogen bonds : bond 0.05075 ( 668) hydrogen bonds : angle 4.51997 ( 2008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.370 Fit side-chains REVERT: A 76 LYS cc_start: 0.6897 (tptt) cc_final: 0.6691 (tptp) REVERT: A 174 MET cc_start: 0.6838 (ptp) cc_final: 0.6467 (ptm) REVERT: A 296 THR cc_start: 0.7819 (OUTLIER) cc_final: 0.7578 (p) REVERT: A 324 HIS cc_start: 0.7819 (t70) cc_final: 0.7399 (t-90) REVERT: B 76 LYS cc_start: 0.6926 (tptt) cc_final: 0.6721 (tptp) REVERT: B 174 MET cc_start: 0.6870 (ptp) cc_final: 0.6497 (ptm) REVERT: B 296 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7570 (p) REVERT: B 324 HIS cc_start: 0.7825 (t70) cc_final: 0.7407 (t-90) REVERT: C 76 LYS cc_start: 0.6901 (tptt) cc_final: 0.6693 (tptp) REVERT: C 174 MET cc_start: 0.6851 (ptp) cc_final: 0.6494 (ptm) REVERT: C 214 ARG cc_start: 0.7380 (ttm-80) cc_final: 0.7175 (mtp85) REVERT: C 296 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7573 (p) REVERT: C 324 HIS cc_start: 0.7843 (t70) cc_final: 0.7421 (t-90) REVERT: D 162 LYS cc_start: 0.6458 (pptt) cc_final: 0.5936 (mtmm) REVERT: D 174 MET cc_start: 0.6791 (ptp) cc_final: 0.6423 (ptm) REVERT: D 214 ARG cc_start: 0.7388 (ttm-80) cc_final: 0.7181 (mtp85) REVERT: D 296 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7574 (p) REVERT: D 324 HIS cc_start: 0.7829 (t70) cc_final: 0.7409 (t-90) outliers start: 20 outliers final: 7 residues processed: 163 average time/residue: 0.9814 time to fit residues: 171.5251 Evaluate side-chains 144 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.174426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.123209 restraints weight = 71453.714| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.27 r_work: 0.3349 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8652 Z= 0.193 Angle : 0.545 5.059 11720 Z= 0.295 Chirality : 0.036 0.133 1260 Planarity : 0.004 0.047 1420 Dihedral : 9.557 72.701 1208 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.32 % Allowed : 27.37 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.26), residues: 1000 helix: 2.24 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.58 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 214 TYR 0.012 0.001 TYR D 74 PHE 0.017 0.002 PHE C 304 TRP 0.007 0.001 TRP A 269 HIS 0.002 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 8652) covalent geometry : angle 0.54522 (11720) hydrogen bonds : bond 0.05798 ( 668) hydrogen bonds : angle 4.53911 ( 2008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.329 Fit side-chains REVERT: A 174 MET cc_start: 0.6917 (ptp) cc_final: 0.6524 (ptm) REVERT: A 324 HIS cc_start: 0.7813 (t70) cc_final: 0.7386 (t-90) REVERT: B 114 THR cc_start: 0.8451 (t) cc_final: 0.7791 (p) REVERT: B 174 MET cc_start: 0.6899 (ptp) cc_final: 0.6504 (ptm) REVERT: B 324 HIS cc_start: 0.7821 (t70) cc_final: 0.7393 (t-90) REVERT: C 174 MET cc_start: 0.6885 (ptp) cc_final: 0.6495 (ptm) REVERT: C 214 ARG cc_start: 0.7583 (ttm-80) cc_final: 0.7298 (mtp85) REVERT: C 324 HIS cc_start: 0.7841 (t70) cc_final: 0.7411 (t-90) REVERT: D 162 LYS cc_start: 0.6497 (pptt) cc_final: 0.5882 (mtmm) REVERT: D 174 MET cc_start: 0.6907 (ptp) cc_final: 0.6513 (ptm) REVERT: D 214 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7328 (mtp85) REVERT: D 324 HIS cc_start: 0.7815 (t70) cc_final: 0.7383 (t-90) outliers start: 28 outliers final: 11 residues processed: 156 average time/residue: 0.9786 time to fit residues: 163.7765 Evaluate side-chains 150 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.175618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.126371 restraints weight = 70662.023| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 3.02 r_work: 0.3375 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8652 Z= 0.146 Angle : 0.513 4.323 11720 Z= 0.276 Chirality : 0.034 0.122 1260 Planarity : 0.004 0.033 1420 Dihedral : 9.309 71.605 1208 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.73 % Allowed : 28.44 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.26), residues: 1000 helix: 2.29 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.78 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 214 TYR 0.010 0.001 TYR D 74 PHE 0.012 0.001 PHE D 297 TRP 0.007 0.001 TRP C 269 HIS 0.002 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8652) covalent geometry : angle 0.51326 (11720) hydrogen bonds : bond 0.05405 ( 668) hydrogen bonds : angle 4.49144 ( 2008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7354 (ppt170) REVERT: A 174 MET cc_start: 0.6919 (ptp) cc_final: 0.6552 (ptm) REVERT: A 230 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7640 (tmtt) REVERT: A 324 HIS cc_start: 0.7817 (t70) cc_final: 0.7382 (t-90) REVERT: B 114 THR cc_start: 0.8436 (t) cc_final: 0.7759 (p) REVERT: B 174 MET cc_start: 0.6840 (ptp) cc_final: 0.6457 (ptm) REVERT: B 230 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7651 (tmtt) REVERT: B 324 HIS cc_start: 0.7817 (t70) cc_final: 0.7382 (t-90) REVERT: C 87 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7354 (ppt170) REVERT: C 174 MET cc_start: 0.6841 (ptp) cc_final: 0.6464 (ptm) REVERT: C 214 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.7331 (mtp85) REVERT: C 230 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7682 (tmtt) REVERT: C 324 HIS cc_start: 0.7833 (t70) cc_final: 0.7396 (t-90) REVERT: D 162 LYS cc_start: 0.6505 (pptt) cc_final: 0.5885 (mtmm) REVERT: D 174 MET cc_start: 0.6849 (ptp) cc_final: 0.6474 (ptm) REVERT: D 214 ARG cc_start: 0.7599 (ttm-80) cc_final: 0.7338 (mtp85) REVERT: D 230 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7674 (tmtt) REVERT: D 324 HIS cc_start: 0.7813 (t70) cc_final: 0.7389 (t-90) outliers start: 23 outliers final: 13 residues processed: 155 average time/residue: 1.0506 time to fit residues: 173.3125 Evaluate side-chains 163 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 323 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.175903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.125258 restraints weight = 69564.694| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.06 r_work: 0.3382 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8652 Z= 0.144 Angle : 0.505 4.123 11720 Z= 0.273 Chirality : 0.034 0.122 1260 Planarity : 0.003 0.031 1420 Dihedral : 9.139 69.425 1207 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.96 % Allowed : 27.84 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.26), residues: 1000 helix: 2.30 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.74 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.010 0.001 TYR D 74 PHE 0.013 0.001 PHE D 297 TRP 0.007 0.001 TRP C 269 HIS 0.002 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8652) covalent geometry : angle 0.50512 (11720) hydrogen bonds : bond 0.05302 ( 668) hydrogen bonds : angle 4.46405 ( 2008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7350 (ppt170) REVERT: A 174 MET cc_start: 0.6884 (ptp) cc_final: 0.6524 (ptm) REVERT: A 296 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7595 (p) REVERT: A 324 HIS cc_start: 0.7812 (t70) cc_final: 0.7383 (t-90) REVERT: B 174 MET cc_start: 0.6877 (ptp) cc_final: 0.6514 (ptm) REVERT: B 296 THR cc_start: 0.7984 (OUTLIER) cc_final: 0.7601 (p) REVERT: B 324 HIS cc_start: 0.7808 (t70) cc_final: 0.7378 (t-90) REVERT: C 87 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7353 (ppt170) REVERT: C 174 MET cc_start: 0.6839 (ptp) cc_final: 0.6474 (ptm) REVERT: C 214 ARG cc_start: 0.7588 (ttm-80) cc_final: 0.7317 (mtp85) REVERT: C 296 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7604 (p) REVERT: C 324 HIS cc_start: 0.7822 (t70) cc_final: 0.7407 (t-90) REVERT: D 162 LYS cc_start: 0.6502 (pptt) cc_final: 0.5891 (mtmm) REVERT: D 174 MET cc_start: 0.6849 (ptp) cc_final: 0.6487 (ptm) REVERT: D 214 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.7323 (mtp85) REVERT: D 296 THR cc_start: 0.7978 (OUTLIER) cc_final: 0.7600 (p) REVERT: D 324 HIS cc_start: 0.7813 (t70) cc_final: 0.7395 (t-90) outliers start: 25 outliers final: 14 residues processed: 167 average time/residue: 1.0755 time to fit residues: 191.7688 Evaluate side-chains 167 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 323 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.176143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.125099 restraints weight = 71286.765| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.07 r_work: 0.3388 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8652 Z= 0.144 Angle : 0.507 4.562 11720 Z= 0.274 Chirality : 0.034 0.122 1260 Planarity : 0.003 0.031 1420 Dihedral : 9.034 68.438 1206 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.32 % Allowed : 28.08 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.63 (0.26), residues: 1000 helix: 2.28 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.75 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.009 0.001 TYR D 74 PHE 0.013 0.001 PHE C 297 TRP 0.007 0.001 TRP A 269 HIS 0.002 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8652) covalent geometry : angle 0.50691 (11720) hydrogen bonds : bond 0.05272 ( 668) hydrogen bonds : angle 4.44250 ( 2008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7345 (ppt170) REVERT: A 174 MET cc_start: 0.6879 (ptp) cc_final: 0.6523 (ptm) REVERT: A 230 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7607 (tmtt) REVERT: A 296 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7576 (p) REVERT: A 324 HIS cc_start: 0.7809 (t70) cc_final: 0.7385 (t-90) REVERT: B 174 MET cc_start: 0.6867 (ptp) cc_final: 0.6510 (ptm) REVERT: B 230 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7614 (tmtt) REVERT: B 324 HIS cc_start: 0.7804 (t70) cc_final: 0.7380 (t-90) REVERT: C 87 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7347 (ppt170) REVERT: C 174 MET cc_start: 0.6835 (ptp) cc_final: 0.6473 (ptm) REVERT: C 214 ARG cc_start: 0.7582 (ttm-80) cc_final: 0.7329 (mtp85) REVERT: C 230 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7629 (tmtt) REVERT: C 324 HIS cc_start: 0.7841 (t70) cc_final: 0.7416 (t-90) REVERT: D 162 LYS cc_start: 0.6506 (pptt) cc_final: 0.5895 (mtmm) REVERT: D 174 MET cc_start: 0.6849 (ptp) cc_final: 0.6492 (ptm) REVERT: D 214 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.7337 (mtp85) REVERT: D 230 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7632 (tmtt) REVERT: D 296 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7567 (p) REVERT: D 324 HIS cc_start: 0.7807 (t70) cc_final: 0.7392 (t-90) outliers start: 28 outliers final: 13 residues processed: 170 average time/residue: 1.0385 time to fit residues: 187.8918 Evaluate side-chains 165 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.4232 r_free = 0.4232 target = 0.178043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.125481 restraints weight = 68740.524| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.42 r_work: 0.3378 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3376 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 0.037 8652 Z= 0.182 Angle : 0.541 4.816 11720 Z= 0.295 Chirality : 0.036 0.132 1260 Planarity : 0.004 0.030 1420 Dihedral : 8.942 65.599 1204 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.32 % Allowed : 27.84 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.26), residues: 1000 helix: 2.17 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.76 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.012 0.001 TYR D 74 PHE 0.015 0.002 PHE A 304 TRP 0.008 0.001 TRP A 269 HIS 0.003 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8652) covalent geometry : angle 0.54087 (11720) hydrogen bonds : bond 0.05644 ( 668) hydrogen bonds : angle 4.47408 ( 2008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7363 (ppt170) REVERT: A 123 GLU cc_start: 0.6709 (pp20) cc_final: 0.6401 (pp20) REVERT: A 174 MET cc_start: 0.6908 (ptp) cc_final: 0.6557 (ptm) REVERT: A 296 THR cc_start: 0.8105 (OUTLIER) cc_final: 0.7705 (p) REVERT: A 324 HIS cc_start: 0.7839 (t70) cc_final: 0.7430 (t-90) REVERT: B 174 MET cc_start: 0.6865 (ptp) cc_final: 0.6497 (ptm) REVERT: B 324 HIS cc_start: 0.7828 (t70) cc_final: 0.7417 (t-90) REVERT: C 87 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7369 (ppt170) REVERT: C 174 MET cc_start: 0.6861 (ptp) cc_final: 0.6505 (ptm) REVERT: C 230 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7709 (tmtt) REVERT: C 324 HIS cc_start: 0.7907 (t70) cc_final: 0.7494 (t-90) REVERT: D 123 GLU cc_start: 0.6722 (pp20) cc_final: 0.6418 (pp20) REVERT: D 162 LYS cc_start: 0.6502 (pptt) cc_final: 0.5933 (mtmm) REVERT: D 174 MET cc_start: 0.6883 (ptp) cc_final: 0.6525 (ptm) REVERT: D 324 HIS cc_start: 0.7830 (t70) cc_final: 0.7425 (t-90) outliers start: 28 outliers final: 15 residues processed: 169 average time/residue: 1.0005 time to fit residues: 180.4990 Evaluate side-chains 165 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 320 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 7.9990 chunk 72 optimal weight: 0.5980 chunk 19 optimal weight: 0.0970 chunk 27 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 GLN C 204 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.179277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126338 restraints weight = 63265.589| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.92 r_work: 0.3423 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8652 Z= 0.142 Angle : 0.522 8.228 11720 Z= 0.281 Chirality : 0.034 0.125 1260 Planarity : 0.004 0.060 1420 Dihedral : 8.803 64.748 1204 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.49 % Allowed : 29.74 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.26), residues: 1000 helix: 2.28 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.81 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 214 TYR 0.009 0.001 TYR D 74 PHE 0.013 0.001 PHE A 297 TRP 0.007 0.001 TRP B 269 HIS 0.002 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8652) covalent geometry : angle 0.52190 (11720) hydrogen bonds : bond 0.05231 ( 668) hydrogen bonds : angle 4.39299 ( 2008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7390 (ppt170) REVERT: A 114 THR cc_start: 0.8400 (t) cc_final: 0.7887 (p) REVERT: A 174 MET cc_start: 0.7048 (ptp) cc_final: 0.6686 (ptm) REVERT: A 296 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7609 (p) REVERT: A 324 HIS cc_start: 0.7907 (t70) cc_final: 0.7503 (t-90) REVERT: B 174 MET cc_start: 0.7001 (ptp) cc_final: 0.6644 (ptm) REVERT: B 324 HIS cc_start: 0.7891 (t70) cc_final: 0.7486 (t-90) REVERT: C 87 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7388 (ppt170) REVERT: C 114 THR cc_start: 0.8419 (t) cc_final: 0.7917 (p) REVERT: C 123 GLU cc_start: 0.6819 (pp20) cc_final: 0.6531 (pp20) REVERT: C 174 MET cc_start: 0.6995 (ptp) cc_final: 0.6622 (ptm) REVERT: C 214 ARG cc_start: 0.7294 (ttm-80) cc_final: 0.7054 (mtp85) REVERT: C 324 HIS cc_start: 0.7901 (t70) cc_final: 0.7496 (t-90) REVERT: D 114 THR cc_start: 0.8428 (t) cc_final: 0.7919 (p) REVERT: D 162 LYS cc_start: 0.6586 (pptt) cc_final: 0.5962 (mtmt) REVERT: D 214 ARG cc_start: 0.7302 (ttm-80) cc_final: 0.7062 (mtp85) REVERT: D 296 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7626 (p) REVERT: D 324 HIS cc_start: 0.7887 (t70) cc_final: 0.7491 (t-90) outliers start: 21 outliers final: 10 residues processed: 171 average time/residue: 0.9854 time to fit residues: 180.1358 Evaluate side-chains 156 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.178203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.124455 restraints weight = 72087.199| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.05 r_work: 0.3399 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8652 Z= 0.164 Angle : 0.537 4.944 11720 Z= 0.291 Chirality : 0.036 0.129 1260 Planarity : 0.004 0.049 1420 Dihedral : 8.746 63.072 1204 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.20 % Allowed : 28.91 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.50 (0.26), residues: 1000 helix: 2.20 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.80 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 207 TYR 0.010 0.001 TYR D 74 PHE 0.014 0.001 PHE D 297 TRP 0.007 0.001 TRP A 269 HIS 0.003 0.001 HIS C 228 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8652) covalent geometry : angle 0.53676 (11720) hydrogen bonds : bond 0.05424 ( 668) hydrogen bonds : angle 4.41578 ( 2008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7345 (ppt170) REVERT: A 114 THR cc_start: 0.8434 (t) cc_final: 0.7959 (p) REVERT: A 123 GLU cc_start: 0.6717 (pp20) cc_final: 0.6314 (pp20) REVERT: A 174 MET cc_start: 0.6887 (ptp) cc_final: 0.6541 (ptm) REVERT: A 296 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7662 (p) REVERT: A 324 HIS cc_start: 0.7906 (t70) cc_final: 0.7507 (t-90) REVERT: B 174 MET cc_start: 0.6816 (ptp) cc_final: 0.6454 (ptm) REVERT: B 324 HIS cc_start: 0.7896 (t70) cc_final: 0.7495 (t-90) REVERT: C 87 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7347 (ppt170) REVERT: C 114 THR cc_start: 0.8417 (t) cc_final: 0.7948 (p) REVERT: C 123 GLU cc_start: 0.6717 (pp20) cc_final: 0.6409 (pp20) REVERT: C 174 MET cc_start: 0.6836 (ptp) cc_final: 0.6491 (ptm) REVERT: C 324 HIS cc_start: 0.7906 (t70) cc_final: 0.7501 (t-90) REVERT: D 114 THR cc_start: 0.8411 (t) cc_final: 0.7930 (p) REVERT: D 123 GLU cc_start: 0.6733 (pp20) cc_final: 0.6346 (pp20) REVERT: D 162 LYS cc_start: 0.6568 (pptt) cc_final: 0.5952 (mtmt) REVERT: D 174 MET cc_start: 0.6859 (ptp) cc_final: 0.6511 (ptm) REVERT: D 296 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7670 (p) REVERT: D 324 HIS cc_start: 0.7893 (t70) cc_final: 0.7501 (t-90) outliers start: 27 outliers final: 17 residues processed: 165 average time/residue: 0.9636 time to fit residues: 170.3054 Evaluate side-chains 163 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 151 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 207 ARG Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 296 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.180061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128947 restraints weight = 72176.259| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.64 r_work: 0.3399 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8652 Z= 0.134 Angle : 0.530 8.554 11720 Z= 0.282 Chirality : 0.035 0.128 1260 Planarity : 0.004 0.046 1420 Dihedral : 8.551 61.846 1204 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.66 % Allowed : 30.09 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.26), residues: 1000 helix: 2.30 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.84 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 214 TYR 0.008 0.001 TYR D 74 PHE 0.013 0.001 PHE A 297 TRP 0.007 0.001 TRP A 269 HIS 0.001 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8652) covalent geometry : angle 0.53045 (11720) hydrogen bonds : bond 0.04982 ( 668) hydrogen bonds : angle 4.36571 ( 2008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7305 (ppt170) REVERT: A 114 THR cc_start: 0.8442 (t) cc_final: 0.7951 (p) REVERT: A 123 GLU cc_start: 0.6693 (pp20) cc_final: 0.6310 (pp20) REVERT: A 174 MET cc_start: 0.6882 (ptp) cc_final: 0.6531 (ptm) REVERT: A 324 HIS cc_start: 0.7878 (t70) cc_final: 0.7484 (t-90) REVERT: B 114 THR cc_start: 0.8383 (t) cc_final: 0.7852 (p) REVERT: B 123 GLU cc_start: 0.6749 (pp20) cc_final: 0.6404 (pp20) REVERT: B 174 MET cc_start: 0.6854 (ptp) cc_final: 0.6496 (ptm) REVERT: B 324 HIS cc_start: 0.7864 (t70) cc_final: 0.7471 (t-90) REVERT: C 87 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.7300 (ppt170) REVERT: C 114 THR cc_start: 0.8407 (t) cc_final: 0.7919 (p) REVERT: C 123 GLU cc_start: 0.6717 (pp20) cc_final: 0.6412 (pp20) REVERT: C 174 MET cc_start: 0.6864 (ptp) cc_final: 0.6494 (ptm) REVERT: C 324 HIS cc_start: 0.7869 (t70) cc_final: 0.7471 (t-90) REVERT: D 114 THR cc_start: 0.8423 (t) cc_final: 0.7930 (p) REVERT: D 123 GLU cc_start: 0.6709 (pp20) cc_final: 0.6339 (pp20) REVERT: D 162 LYS cc_start: 0.6535 (pptt) cc_final: 0.5920 (mtmm) REVERT: D 174 MET cc_start: 0.6864 (ptp) cc_final: 0.6508 (ptm) REVERT: D 324 HIS cc_start: 0.7869 (t70) cc_final: 0.7478 (t-90) outliers start: 14 outliers final: 10 residues processed: 164 average time/residue: 0.9553 time to fit residues: 168.5117 Evaluate side-chains 159 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 176 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.179203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128595 restraints weight = 71449.517| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.63 r_work: 0.3384 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8652 Z= 0.149 Angle : 0.519 5.210 11720 Z= 0.280 Chirality : 0.035 0.124 1260 Planarity : 0.004 0.043 1420 Dihedral : 8.537 61.074 1204 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.66 % Allowed : 30.21 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.26), residues: 1000 helix: 2.27 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.77 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 207 TYR 0.010 0.001 TYR D 74 PHE 0.014 0.001 PHE C 297 TRP 0.007 0.001 TRP A 269 HIS 0.003 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8652) covalent geometry : angle 0.51862 (11720) hydrogen bonds : bond 0.05164 ( 668) hydrogen bonds : angle 4.36823 ( 2008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6496.86 seconds wall clock time: 110 minutes 8.73 seconds (6608.73 seconds total)