Starting phenix.real_space_refine on Tue Jan 21 12:42:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8izy_35877/01_2025/8izy_35877_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8izy_35877/01_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_35877/01_2025/8izy_35877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8izy_35877/01_2025/8izy_35877.map" model { file = "/net/cci-nas-00/data/ceres_data/8izy_35877/01_2025/8izy_35877_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8izy_35877/01_2025/8izy_35877_neut_trim.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 13.91, per 1000 atoms: 0.83 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: 4.23 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.03 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: 5.52 Time building geometry restraints manager: 5.03 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 330 or resid 801)) selection = (chain 'B' and (resid 70 through 131 or resid 133 through 330 or resid 801)) selection = (chain 'C' and (resid 70 through 131 or resid 133 through 330 or resid 801)) selection = (chain 'D' and (resid 70 through 131 or resid 133 through 330 or resid 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: 1.160 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: 0.290 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 41.780 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 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:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.370 ------------------------------------------------------------------------------- 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= 0.366 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 : 7.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP D 269 HIS 0.002 0.001 HIS C 324 PHE 0.009 0.001 PHE D 100 TYR 0.008 0.001 TYR D 74 ARG 0.008 0.000 ARG D 214 *********************** 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 : 1.158 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: 2.4531 time to fit residues: 400.4767 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 : 1.268 ------------------------------------------------------------------------------- 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 84 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 0.0010 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.0388 ------------------------------------------------------------------------------- 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 = 0.176722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121379 restraints weight = 67827.941| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.45 r_work: 0.3422 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.0889 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= 0.187 Angle : 0.510 5.854 11720 Z= 0.272 Chirality : 0.034 0.122 1260 Planarity : 0.004 0.045 1420 Dihedral : 9.760 78.339 1208 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.73 % Allowed : 28.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.26), residues: 1000 helix: 2.37 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.42 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 269 HIS 0.003 0.001 HIS D 228 PHE 0.012 0.001 PHE A 297 TYR 0.009 0.001 TYR A 82 ARG 0.006 0.000 ARG A 214 *********************** 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 169 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.231 Fit side-chains REVERT: A 76 LYS cc_start: 0.6913 (tptt) cc_final: 0.6700 (tptp) REVERT: A 174 MET cc_start: 0.6928 (ptp) cc_final: 0.6558 (ptm) REVERT: A 214 ARG cc_start: 0.7522 (ttm-80) cc_final: 0.7281 (mtp85) REVERT: A 296 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7691 (p) REVERT: A 324 HIS cc_start: 0.7844 (t70) cc_final: 0.7415 (t-90) REVERT: B 76 LYS cc_start: 0.6896 (tptt) cc_final: 0.6684 (tptp) REVERT: B 174 MET cc_start: 0.6958 (ptp) cc_final: 0.6580 (ptm) REVERT: B 214 ARG cc_start: 0.7513 (ttm-80) cc_final: 0.7278 (mtp85) REVERT: B 296 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7654 (p) REVERT: B 324 HIS cc_start: 0.7848 (t70) cc_final: 0.7420 (t-90) REVERT: C 76 LYS cc_start: 0.6926 (tptt) cc_final: 0.6709 (tptp) REVERT: C 174 MET cc_start: 0.6942 (ptp) cc_final: 0.6570 (ptm) REVERT: C 214 ARG cc_start: 0.7547 (ttm-80) cc_final: 0.7292 (mtp85) REVERT: C 296 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7662 (p) REVERT: C 324 HIS cc_start: 0.7859 (t70) cc_final: 0.7428 (t-90) REVERT: D 162 LYS cc_start: 0.6483 (pptt) cc_final: 0.5946 (mtmm) REVERT: D 174 MET cc_start: 0.6896 (ptp) cc_final: 0.6527 (ptm) REVERT: D 214 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7289 (mtp85) REVERT: D 296 THR cc_start: 0.7902 (OUTLIER) cc_final: 0.7654 (p) REVERT: D 324 HIS cc_start: 0.7850 (t70) cc_final: 0.7421 (t-90) outliers start: 23 outliers final: 7 residues processed: 163 average time/residue: 2.2698 time to fit residues: 399.3393 Evaluate side-chains 143 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.177142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.125325 restraints weight = 70777.487| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.12 r_work: 0.3405 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 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 = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1080 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= 0.181 Angle : 0.493 5.061 11720 Z= 0.264 Chirality : 0.034 0.119 1260 Planarity : 0.004 0.032 1420 Dihedral : 9.528 76.960 1208 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.49 % Allowed : 28.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.27), residues: 1000 helix: 2.36 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.44 (0.56), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 270 HIS 0.002 0.001 HIS D 228 PHE 0.013 0.001 PHE D 163 TYR 0.009 0.001 TYR D 74 ARG 0.004 0.000 ARG D 214 *********************** 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 165 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.283 Fit side-chains REVERT: A 174 MET cc_start: 0.6833 (ptp) cc_final: 0.6445 (ptm) REVERT: A 214 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7281 (mtp85) REVERT: A 296 THR cc_start: 0.7799 (OUTLIER) cc_final: 0.7545 (p) REVERT: A 324 HIS cc_start: 0.7798 (t70) cc_final: 0.7378 (t-90) REVERT: B 174 MET cc_start: 0.6889 (ptp) cc_final: 0.6510 (ptm) REVERT: B 214 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.7286 (mtp85) REVERT: B 296 THR cc_start: 0.7795 (OUTLIER) cc_final: 0.7544 (p) REVERT: B 324 HIS cc_start: 0.7800 (t70) cc_final: 0.7381 (t-90) REVERT: C 174 MET cc_start: 0.6872 (ptp) cc_final: 0.6500 (ptm) REVERT: C 214 ARG cc_start: 0.7527 (ttm-80) cc_final: 0.7290 (mtp85) REVERT: C 324 HIS cc_start: 0.7812 (t70) cc_final: 0.7392 (t-90) REVERT: D 162 LYS cc_start: 0.6476 (pptt) cc_final: 0.5890 (mtmm) REVERT: D 174 MET cc_start: 0.6817 (ptp) cc_final: 0.6451 (ptm) REVERT: D 214 ARG cc_start: 0.7533 (ttm-80) cc_final: 0.7293 (mtp85) REVERT: D 296 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7537 (p) REVERT: D 324 HIS cc_start: 0.7800 (t70) cc_final: 0.7378 (t-90) outliers start: 21 outliers final: 6 residues processed: 157 average time/residue: 2.2877 time to fit residues: 385.7237 Evaluate side-chains 143 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 296 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 135 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 97 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.175710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.125960 restraints weight = 71896.108| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.34 r_work: 0.3374 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8652 Z= 0.240 Angle : 0.516 4.857 11720 Z= 0.278 Chirality : 0.035 0.131 1260 Planarity : 0.004 0.029 1420 Dihedral : 9.461 72.575 1207 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.73 % Allowed : 27.84 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.26), residues: 1000 helix: 2.30 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.52 (0.54), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 269 HIS 0.003 0.001 HIS D 228 PHE 0.014 0.002 PHE A 297 TYR 0.010 0.001 TYR D 74 ARG 0.003 0.000 ARG D 214 *********************** 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 : 1.242 Fit side-chains REVERT: A 87 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7313 (ppt170) REVERT: A 174 MET cc_start: 0.6915 (ptp) cc_final: 0.6545 (ptm) REVERT: A 214 ARG cc_start: 0.7513 (ttm-80) cc_final: 0.7275 (mtp85) REVERT: A 324 HIS cc_start: 0.7806 (t70) cc_final: 0.7368 (t-90) REVERT: B 174 MET cc_start: 0.6858 (ptp) cc_final: 0.6472 (ptm) REVERT: B 214 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7256 (mtp85) REVERT: B 324 HIS cc_start: 0.7807 (t70) cc_final: 0.7369 (t-90) REVERT: C 87 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7315 (ppt170) REVERT: C 174 MET cc_start: 0.6843 (ptp) cc_final: 0.6461 (ptm) REVERT: C 214 ARG cc_start: 0.7551 (ttm-80) cc_final: 0.7286 (mtp85) REVERT: C 324 HIS cc_start: 0.7822 (t70) cc_final: 0.7401 (t-90) REVERT: D 162 LYS cc_start: 0.6473 (pptt) cc_final: 0.5910 (mtmm) REVERT: D 174 MET cc_start: 0.6849 (ptp) cc_final: 0.6481 (ptm) REVERT: D 214 ARG cc_start: 0.7551 (ttm-80) cc_final: 0.7288 (mtp85) REVERT: D 324 HIS cc_start: 0.7808 (t70) cc_final: 0.7383 (t-90) outliers start: 23 outliers final: 8 residues processed: 157 average time/residue: 2.4625 time to fit residues: 412.7609 Evaluate side-chains 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 B residue 113 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 113 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 68 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.4231 r_free = 0.4231 target = 0.177097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.124047 restraints weight = 70970.581| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.89 r_work: 0.3406 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- 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 = 0.10 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 = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8652 Z= 0.167 Angle : 0.487 4.532 11720 Z= 0.260 Chirality : 0.033 0.112 1260 Planarity : 0.003 0.031 1420 Dihedral : 9.199 73.696 1206 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.37 % Allowed : 27.96 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.26), residues: 1000 helix: 2.36 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.61 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 270 HIS 0.001 0.001 HIS D 228 PHE 0.012 0.001 PHE A 297 TYR 0.008 0.001 TYR D 74 ARG 0.003 0.000 ARG D 214 *********************** 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 167 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7286 (ppt170) REVERT: A 174 MET cc_start: 0.6833 (ptp) cc_final: 0.6461 (ptm) REVERT: A 214 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.7257 (mtp85) REVERT: A 296 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7552 (p) REVERT: A 324 HIS cc_start: 0.7803 (t70) cc_final: 0.7376 (t-90) REVERT: B 174 MET cc_start: 0.6797 (ptp) cc_final: 0.6416 (ptm) REVERT: B 214 ARG cc_start: 0.7489 (ttm-80) cc_final: 0.7259 (mtp85) REVERT: B 296 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7553 (p) REVERT: B 324 HIS cc_start: 0.7799 (t70) cc_final: 0.7371 (t-90) REVERT: C 87 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7282 (ppt170) REVERT: C 174 MET cc_start: 0.6804 (ptp) cc_final: 0.6424 (ptm) REVERT: C 214 ARG cc_start: 0.7529 (ttm-80) cc_final: 0.7273 (mtp85) REVERT: C 230 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7583 (tmtt) REVERT: C 324 HIS cc_start: 0.7816 (t70) cc_final: 0.7386 (t-90) REVERT: D 162 LYS cc_start: 0.6519 (pptt) cc_final: 0.5902 (mtmm) REVERT: D 174 MET cc_start: 0.6806 (ptp) cc_final: 0.6437 (ptm) REVERT: D 214 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.7302 (mtp85) REVERT: D 230 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7582 (tmtt) REVERT: D 296 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7555 (p) REVERT: D 324 HIS cc_start: 0.7794 (t70) cc_final: 0.7359 (t-90) outliers start: 20 outliers final: 11 residues processed: 160 average time/residue: 2.4368 time to fit residues: 416.1253 Evaluate side-chains 161 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 296 THR Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 113 SER 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 81 LEU Chi-restraints excluded: chain C residue 87 ARG 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.176107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.124282 restraints weight = 71950.232| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 3.15 r_work: 0.3377 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1448 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= 0.268 Angle : 0.528 4.891 11720 Z= 0.287 Chirality : 0.036 0.132 1260 Planarity : 0.004 0.030 1420 Dihedral : 9.028 68.398 1204 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.84 % Allowed : 28.20 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.26), residues: 1000 helix: 2.26 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.61 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 269 HIS 0.003 0.001 HIS D 228 PHE 0.017 0.002 PHE C 304 TYR 0.012 0.001 TYR D 74 ARG 0.002 0.000 ARG B 87 *********************** 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 173 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7287 (ppt170) REVERT: A 174 MET cc_start: 0.6832 (ptp) cc_final: 0.6479 (ptm) REVERT: A 214 ARG cc_start: 0.7537 (ttm-80) cc_final: 0.7286 (mtp85) REVERT: A 324 HIS cc_start: 0.7853 (t70) cc_final: 0.7434 (t-90) REVERT: B 114 THR cc_start: 0.8390 (t) cc_final: 0.7895 (p) REVERT: B 174 MET cc_start: 0.6859 (ptp) cc_final: 0.6497 (ptm) REVERT: B 214 ARG cc_start: 0.7513 (ttm-80) cc_final: 0.7265 (mtp85) REVERT: B 324 HIS cc_start: 0.7832 (t70) cc_final: 0.7409 (t-90) REVERT: C 87 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7294 (ppt170) REVERT: C 174 MET cc_start: 0.6833 (ptp) cc_final: 0.6475 (ptm) REVERT: C 214 ARG cc_start: 0.7574 (ttm-80) cc_final: 0.7311 (mtp85) REVERT: C 230 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7728 (tmtt) REVERT: C 324 HIS cc_start: 0.7901 (t70) cc_final: 0.7480 (t-90) REVERT: D 162 LYS cc_start: 0.6495 (pptt) cc_final: 0.5930 (mtmm) REVERT: D 174 MET cc_start: 0.6831 (ptp) cc_final: 0.6472 (ptm) REVERT: D 214 ARG cc_start: 0.7576 (ttm-80) cc_final: 0.7310 (mtp85) REVERT: D 230 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7710 (tmtt) REVERT: D 324 HIS cc_start: 0.7827 (t70) cc_final: 0.7396 (t-90) outliers start: 24 outliers final: 12 residues processed: 165 average time/residue: 2.7007 time to fit residues: 474.1817 Evaluate side-chains 164 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 B residue 113 SER Chi-restraints excluded: chain B residue 135 VAL 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 176 LEU Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 230 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 35 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.178494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.123960 restraints weight = 70048.162| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.45 r_work: 0.3389 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.003 0.039 8652 Z= 0.223 Angle : 0.542 7.483 11720 Z= 0.290 Chirality : 0.035 0.125 1260 Planarity : 0.004 0.030 1420 Dihedral : 8.886 66.971 1204 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.84 % Allowed : 28.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.26), residues: 1000 helix: 2.30 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.77 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 269 HIS 0.002 0.001 HIS C 228 PHE 0.013 0.001 PHE D 297 TYR 0.010 0.001 TYR D 74 ARG 0.002 0.000 ARG C 214 *********************** 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 173 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7336 (ppt170) REVERT: A 114 THR cc_start: 0.8343 (t) cc_final: 0.7861 (p) REVERT: A 174 MET cc_start: 0.6828 (ptp) cc_final: 0.6470 (ptm) REVERT: A 214 ARG cc_start: 0.7538 (ttm-80) cc_final: 0.7298 (mtp85) REVERT: A 324 HIS cc_start: 0.7877 (t70) cc_final: 0.7469 (t-90) REVERT: B 114 THR cc_start: 0.8411 (t) cc_final: 0.7928 (p) REVERT: B 174 MET cc_start: 0.6843 (ptp) cc_final: 0.6486 (ptm) REVERT: B 214 ARG cc_start: 0.7536 (ttm-80) cc_final: 0.7304 (mtp85) REVERT: B 324 HIS cc_start: 0.7881 (t70) cc_final: 0.7475 (t-90) REVERT: C 87 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7342 (ppt170) REVERT: C 114 THR cc_start: 0.8341 (t) cc_final: 0.7859 (p) REVERT: C 174 MET cc_start: 0.6812 (ptp) cc_final: 0.6454 (ptm) REVERT: C 324 HIS cc_start: 0.7911 (t70) cc_final: 0.7495 (t-90) REVERT: D 114 THR cc_start: 0.8389 (t) cc_final: 0.7911 (p) REVERT: D 162 LYS cc_start: 0.6474 (pptt) cc_final: 0.5920 (mtmm) REVERT: D 324 HIS cc_start: 0.7868 (t70) cc_final: 0.7451 (t-90) outliers start: 24 outliers final: 17 residues processed: 165 average time/residue: 2.5365 time to fit residues: 446.1914 Evaluate side-chains 159 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 113 SER 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 B residue 323 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.178525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.124054 restraints weight = 64729.716| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.86 r_work: 0.3405 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8652 Z= 0.232 Angle : 0.523 4.234 11720 Z= 0.285 Chirality : 0.035 0.129 1260 Planarity : 0.004 0.057 1420 Dihedral : 8.804 64.789 1204 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.67 % Allowed : 28.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.26), residues: 1000 helix: 2.26 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.78 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 269 HIS 0.002 0.001 HIS C 228 PHE 0.013 0.001 PHE A 297 TYR 0.010 0.001 TYR D 74 ARG 0.008 0.000 ARG C 214 *********************** 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 178 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7314 (ppt170) REVERT: A 114 THR cc_start: 0.8378 (t) cc_final: 0.7901 (p) REVERT: A 174 MET cc_start: 0.6896 (ptp) cc_final: 0.6548 (ptm) REVERT: A 214 ARG cc_start: 0.7534 (ttm-80) cc_final: 0.7283 (mtp85) REVERT: A 296 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7643 (p) REVERT: A 324 HIS cc_start: 0.7844 (t70) cc_final: 0.7425 (t-90) REVERT: B 114 THR cc_start: 0.8417 (t) cc_final: 0.7933 (p) REVERT: B 174 MET cc_start: 0.6866 (ptp) cc_final: 0.6513 (ptm) REVERT: B 214 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.7280 (mtp85) REVERT: B 296 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7645 (p) REVERT: B 324 HIS cc_start: 0.7870 (t70) cc_final: 0.7447 (t-90) REVERT: C 87 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7295 (ppt170) REVERT: C 114 THR cc_start: 0.8376 (t) cc_final: 0.7901 (p) REVERT: C 174 MET cc_start: 0.6855 (ptp) cc_final: 0.6495 (ptm) REVERT: C 324 HIS cc_start: 0.7891 (t70) cc_final: 0.7481 (t-90) REVERT: D 114 THR cc_start: 0.8409 (t) cc_final: 0.7931 (p) REVERT: D 162 LYS cc_start: 0.6475 (pptt) cc_final: 0.5928 (mtmt) REVERT: D 296 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7652 (p) REVERT: D 324 HIS cc_start: 0.7824 (t70) cc_final: 0.7407 (t-90) outliers start: 31 outliers final: 19 residues processed: 168 average time/residue: 2.4763 time to fit residues: 443.9492 Evaluate side-chains 168 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 296 THR Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 113 SER 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 B residue 296 THR Chi-restraints excluded: chain B residue 323 GLN 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 209 ILE 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 5 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.179192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127495 restraints weight = 69534.523| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 3.47 r_work: 0.3390 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8652 Z= 0.197 Angle : 0.517 5.318 11720 Z= 0.279 Chirality : 0.035 0.120 1260 Planarity : 0.004 0.038 1420 Dihedral : 8.725 64.083 1204 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.96 % Allowed : 28.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.26), residues: 1000 helix: 2.29 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.83 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 269 HIS 0.002 0.001 HIS D 228 PHE 0.013 0.001 PHE B 297 TYR 0.009 0.001 TYR D 74 ARG 0.014 0.000 ARG D 214 *********************** 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 177 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7316 (ppt170) REVERT: A 114 THR cc_start: 0.8444 (t) cc_final: 0.7966 (p) REVERT: A 174 MET cc_start: 0.6930 (ptp) cc_final: 0.6580 (ptm) REVERT: A 214 ARG cc_start: 0.7567 (ttm-80) cc_final: 0.7299 (mtp85) REVERT: A 296 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7598 (p) REVERT: A 324 HIS cc_start: 0.7887 (t70) cc_final: 0.7474 (t-90) REVERT: B 114 THR cc_start: 0.8424 (t) cc_final: 0.7927 (p) REVERT: B 174 MET cc_start: 0.6883 (ptp) cc_final: 0.6522 (ptm) REVERT: B 214 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.7295 (mtp85) REVERT: B 296 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7596 (p) REVERT: B 324 HIS cc_start: 0.7880 (t70) cc_final: 0.7465 (t-90) REVERT: C 87 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7331 (ppt170) REVERT: C 114 THR cc_start: 0.8441 (t) cc_final: 0.7961 (p) REVERT: C 174 MET cc_start: 0.6894 (ptp) cc_final: 0.6531 (ptm) REVERT: C 324 HIS cc_start: 0.7897 (t70) cc_final: 0.7477 (t-90) REVERT: D 114 THR cc_start: 0.8448 (t) cc_final: 0.7967 (p) REVERT: D 162 LYS cc_start: 0.6482 (pptt) cc_final: 0.5932 (mtmt) REVERT: D 296 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7602 (p) REVERT: D 324 HIS cc_start: 0.7840 (t70) cc_final: 0.7428 (t-90) REVERT: D 325 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.5776 (ptp-170) outliers start: 25 outliers final: 13 residues processed: 173 average time/residue: 2.3128 time to fit residues: 429.9045 Evaluate side-chains 164 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 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 176 LEU Chi-restraints excluded: chain B residue 296 THR 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 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 296 THR Chi-restraints excluded: chain D residue 325 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.179270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124532 restraints weight = 71039.259| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.94 r_work: 0.3437 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8652 Z= 0.182 Angle : 0.546 8.170 11720 Z= 0.288 Chirality : 0.035 0.134 1260 Planarity : 0.004 0.039 1420 Dihedral : 8.565 62.899 1204 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.01 % Allowed : 29.50 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.26), residues: 1000 helix: 2.36 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.76 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 270 HIS 0.002 0.001 HIS D 228 PHE 0.013 0.001 PHE A 297 TYR 0.008 0.001 TYR D 74 ARG 0.008 0.000 ARG D 214 ********************** 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 166 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7257 (ppt170) REVERT: A 114 THR cc_start: 0.8448 (t) cc_final: 0.7986 (p) REVERT: A 123 GLU cc_start: 0.6696 (pp20) cc_final: 0.6315 (pp20) REVERT: A 174 MET cc_start: 0.6799 (ptp) cc_final: 0.6450 (ptm) REVERT: A 214 ARG cc_start: 0.7494 (ttm-80) cc_final: 0.7255 (mtp85) REVERT: A 324 HIS cc_start: 0.7851 (t70) cc_final: 0.7440 (t-90) REVERT: B 114 THR cc_start: 0.8407 (t) cc_final: 0.7900 (p) REVERT: B 174 MET cc_start: 0.6796 (ptp) cc_final: 0.6425 (ptm) REVERT: B 214 ARG cc_start: 0.7497 (ttm-80) cc_final: 0.7261 (mtp85) REVERT: B 324 HIS cc_start: 0.7819 (t70) cc_final: 0.7405 (t-90) REVERT: C 87 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7255 (ppt170) REVERT: C 114 THR cc_start: 0.8434 (t) cc_final: 0.7972 (p) REVERT: C 123 GLU cc_start: 0.6676 (pp20) cc_final: 0.6298 (pp20) REVERT: C 174 MET cc_start: 0.6736 (ptp) cc_final: 0.6366 (ptm) REVERT: C 324 HIS cc_start: 0.7864 (t70) cc_final: 0.7444 (t-90) REVERT: D 114 THR cc_start: 0.8451 (t) cc_final: 0.7984 (p) REVERT: D 162 LYS cc_start: 0.6466 (pptt) cc_final: 0.5923 (mtmt) REVERT: D 174 MET cc_start: 0.6766 (ptp) cc_final: 0.6409 (ptm) REVERT: D 324 HIS cc_start: 0.7814 (t70) cc_final: 0.7406 (t-90) outliers start: 17 outliers final: 10 residues processed: 162 average time/residue: 2.4107 time to fit residues: 417.8730 Evaluate side-chains 161 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 135 VAL 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 68 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.180501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.128683 restraints weight = 77662.523| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.68 r_work: 0.3404 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1616 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= 0.170 Angle : 0.502 5.937 11720 Z= 0.269 Chirality : 0.034 0.112 1260 Planarity : 0.004 0.047 1420 Dihedral : 8.512 62.148 1204 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.42 % Allowed : 30.09 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.26), residues: 1000 helix: 2.36 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.80 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 270 HIS 0.002 0.001 HIS D 228 PHE 0.013 0.001 PHE C 297 TYR 0.008 0.001 TYR D 74 ARG 0.008 0.000 ARG D 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13841.46 seconds wall clock time: 242 minutes 42.09 seconds (14562.09 seconds total)