Starting phenix.real_space_refine on Mon Nov 18 15:53:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izy_35877/11_2024/8izy_35877_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izy_35877/11_2024/8izy_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izy_35877/11_2024/8izy_35877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izy_35877/11_2024/8izy_35877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izy_35877/11_2024/8izy_35877_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izy_35877/11_2024/8izy_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 15.07, per 1000 atoms: 0.90 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: 4.94 Conformation dependent library (CDL) restraints added in 2.3 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: 1.15 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: 5.62 Time building geometry restraints manager: 5.71 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: 0.980 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: 0.290 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 44.740 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:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.440 ------------------------------------------------------------------------------- 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 : 1.283 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: 2.4302 time to fit residues: 397.5844 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 : 1.487 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 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 : 1.429 Fit side-chains REVERT: A 76 LYS cc_start: 0.6812 (tptt) cc_final: 0.6607 (tptp) REVERT: A 174 MET cc_start: 0.6864 (ptp) cc_final: 0.6466 (ptm) REVERT: A 296 THR cc_start: 0.7855 (OUTLIER) cc_final: 0.7589 (p) REVERT: A 324 HIS cc_start: 0.7643 (t70) cc_final: 0.7209 (t-90) REVERT: B 76 LYS cc_start: 0.6808 (tptt) cc_final: 0.6605 (tptp) REVERT: B 174 MET cc_start: 0.6895 (ptp) cc_final: 0.6489 (ptm) REVERT: B 296 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7551 (p) REVERT: B 324 HIS cc_start: 0.7635 (t70) cc_final: 0.7202 (t-90) REVERT: C 76 LYS cc_start: 0.6822 (tptt) cc_final: 0.6614 (tptp) REVERT: C 174 MET cc_start: 0.6851 (ptp) cc_final: 0.6455 (ptm) REVERT: C 214 ARG cc_start: 0.7400 (ttm-80) cc_final: 0.7179 (mtp85) REVERT: C 296 THR cc_start: 0.7814 (OUTLIER) cc_final: 0.7554 (p) REVERT: C 324 HIS cc_start: 0.7641 (t70) cc_final: 0.7201 (t-90) REVERT: D 162 LYS cc_start: 0.6456 (pptt) cc_final: 0.5930 (mtmm) REVERT: D 174 MET cc_start: 0.6831 (ptp) cc_final: 0.6436 (ptm) REVERT: D 214 ARG cc_start: 0.7403 (ttm-80) cc_final: 0.7181 (mtp85) REVERT: D 296 THR cc_start: 0.7809 (OUTLIER) cc_final: 0.7548 (p) REVERT: D 324 HIS cc_start: 0.7628 (t70) cc_final: 0.7190 (t-90) outliers start: 23 outliers final: 7 residues processed: 163 average time/residue: 2.2318 time to fit residues: 391.4253 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 : 1.305 ------------------------------------------------------------------------------- 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 50 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1135 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= 0.198 Angle : 0.504 4.870 11720 Z= 0.270 Chirality : 0.034 0.124 1260 Planarity : 0.004 0.041 1420 Dihedral : 9.624 76.514 1208 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.73 % Allowed : 27.73 % Favored : 69.55 % 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: 2.75 (0.27), residues: 1000 helix: 2.33 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.48 (0.55), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 269 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 0.008 0.000 ARG A 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 167 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.549 Fit side-chains REVERT: A 87 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7315 (ppt170) REVERT: A 174 MET cc_start: 0.6844 (ptp) cc_final: 0.6426 (ptm) REVERT: A 324 HIS cc_start: 0.7637 (t70) cc_final: 0.7207 (t-90) REVERT: B 174 MET cc_start: 0.6884 (ptp) cc_final: 0.6472 (ptm) REVERT: B 324 HIS cc_start: 0.7631 (t70) cc_final: 0.7201 (t-90) REVERT: C 87 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7318 (ppt170) REVERT: C 174 MET cc_start: 0.6885 (ptp) cc_final: 0.6488 (ptm) REVERT: C 214 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.7168 (mtp85) REVERT: C 324 HIS cc_start: 0.7638 (t70) cc_final: 0.7203 (t-90) REVERT: D 162 LYS cc_start: 0.6475 (pptt) cc_final: 0.5891 (mtmm) REVERT: D 174 MET cc_start: 0.6862 (ptp) cc_final: 0.6479 (ptm) REVERT: D 214 ARG cc_start: 0.7423 (ttm-80) cc_final: 0.7171 (mtp85) REVERT: D 324 HIS cc_start: 0.7623 (t70) cc_final: 0.7190 (t-90) outliers start: 23 outliers final: 7 residues processed: 156 average time/residue: 2.3084 time to fit residues: 387.2025 Evaluate side-chains 144 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 209 ILE 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 D residue 113 SER Chi-restraints excluded: chain D residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 0.2980 chunk 10 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 91 optimal weight: 0.3980 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1310 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= 0.227 Angle : 0.507 4.460 11720 Z= 0.274 Chirality : 0.035 0.128 1260 Planarity : 0.004 0.030 1420 Dihedral : 9.327 73.238 1207 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.61 % Allowed : 27.96 % 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: 2.72 (0.27), residues: 1000 helix: 2.32 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.57 (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 0.013 0.001 PHE C 297 TYR 0.010 0.001 TYR D 74 ARG 0.005 0.000 ARG A 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 162 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.194 Fit side-chains REVERT: A 87 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7256 (ppt170) REVERT: A 174 MET cc_start: 0.6940 (ptp) cc_final: 0.6549 (ptm) REVERT: A 324 HIS cc_start: 0.7637 (t70) cc_final: 0.7192 (t-90) REVERT: B 174 MET cc_start: 0.6879 (ptp) cc_final: 0.6467 (ptm) REVERT: B 324 HIS cc_start: 0.7632 (t70) cc_final: 0.7186 (t-90) REVERT: C 87 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7261 (ppt170) REVERT: C 174 MET cc_start: 0.6841 (ptp) cc_final: 0.6434 (ptm) REVERT: C 214 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.7160 (mtp85) REVERT: C 324 HIS cc_start: 0.7638 (t70) cc_final: 0.7205 (t-90) REVERT: D 162 LYS cc_start: 0.6465 (pptt) cc_final: 0.5863 (mtmm) REVERT: D 174 MET cc_start: 0.6881 (ptp) cc_final: 0.6489 (ptm) REVERT: D 214 ARG cc_start: 0.7424 (ttm-80) cc_final: 0.7161 (mtp85) REVERT: D 324 HIS cc_start: 0.7625 (t70) cc_final: 0.7192 (t-90) outliers start: 22 outliers final: 7 residues processed: 155 average time/residue: 2.3008 time to fit residues: 382.6556 Evaluate side-chains 148 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 1.330 ------------------------------------------------------------------------------- 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 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 71 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1321 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= 0.283 Angle : 0.537 4.715 11720 Z= 0.291 Chirality : 0.036 0.134 1260 Planarity : 0.004 0.030 1420 Dihedral : 9.256 69.562 1206 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.08 % Allowed : 27.49 % 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: 2.56 (0.26), residues: 1000 helix: 2.22 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.66 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 269 HIS 0.003 0.001 HIS C 228 PHE 0.016 0.002 PHE B 304 TYR 0.012 0.001 TYR D 74 ARG 0.004 0.000 ARG A 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 170 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7270 (ppt170) REVERT: A 174 MET cc_start: 0.6931 (ptp) cc_final: 0.6550 (ptm) REVERT: A 324 HIS cc_start: 0.7652 (t70) cc_final: 0.7207 (t-90) REVERT: B 174 MET cc_start: 0.6901 (ptp) cc_final: 0.6511 (ptm) REVERT: B 324 HIS cc_start: 0.7645 (t70) cc_final: 0.7198 (t-90) REVERT: C 87 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7286 (ppt170) REVERT: C 174 MET cc_start: 0.6878 (ptp) cc_final: 0.6487 (ptm) REVERT: C 324 HIS cc_start: 0.7651 (t70) cc_final: 0.7201 (t-90) REVERT: D 162 LYS cc_start: 0.6482 (pptt) cc_final: 0.5923 (mtmm) REVERT: D 174 MET cc_start: 0.6909 (ptp) cc_final: 0.6529 (ptm) REVERT: D 324 HIS cc_start: 0.7632 (t70) cc_final: 0.7195 (t-90) outliers start: 26 outliers final: 16 residues processed: 161 average time/residue: 2.5351 time to fit residues: 435.2217 Evaluate side-chains 162 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 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 207 ARG 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 207 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.0000 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1454 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= 0.215 Angle : 0.511 4.058 11720 Z= 0.277 Chirality : 0.034 0.125 1260 Planarity : 0.004 0.050 1420 Dihedral : 9.056 68.013 1206 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.25 % Allowed : 29.38 % Favored : 68.36 % 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: 2.63 (0.26), residues: 1000 helix: 2.28 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.74 (0.51), 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 0.013 0.001 PHE D 297 TYR 0.010 0.001 TYR D 74 ARG 0.007 0.000 ARG C 214 *********************** 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 162 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7256 (ppt170) REVERT: A 174 MET cc_start: 0.6917 (ptp) cc_final: 0.6538 (ptm) REVERT: A 324 HIS cc_start: 0.7640 (t70) cc_final: 0.7203 (t-90) REVERT: B 114 THR cc_start: 0.8375 (t) cc_final: 0.7899 (p) REVERT: B 174 MET cc_start: 0.6933 (ptp) cc_final: 0.6553 (ptm) REVERT: B 324 HIS cc_start: 0.7631 (t70) cc_final: 0.7192 (t-90) REVERT: C 87 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7263 (ppt170) REVERT: C 174 MET cc_start: 0.6868 (ptp) cc_final: 0.6481 (ptm) REVERT: C 324 HIS cc_start: 0.7641 (t70) cc_final: 0.7198 (t-90) REVERT: D 162 LYS cc_start: 0.6533 (pptt) cc_final: 0.5913 (mtmm) REVERT: D 174 MET cc_start: 0.6895 (ptp) cc_final: 0.6523 (ptm) REVERT: D 324 HIS cc_start: 0.7665 (t70) cc_final: 0.7220 (t-90) outliers start: 19 outliers final: 10 residues processed: 156 average time/residue: 2.4642 time to fit residues: 411.6145 Evaluate side-chains 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 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 D residue 113 SER Chi-restraints excluded: chain D residue 176 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8652 Z= 0.176 Angle : 0.502 4.710 11720 Z= 0.271 Chirality : 0.034 0.115 1260 Planarity : 0.003 0.031 1420 Dihedral : 8.864 67.371 1204 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.54 % Allowed : 30.09 % Favored : 68.36 % 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: 2.69 (0.26), residues: 1000 helix: 2.33 (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 0.006 0.001 TRP D 270 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 0.008 0.000 ARG D 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 163 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 1.518 Fit side-chains revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7247 (ppt170) REVERT: A 174 MET cc_start: 0.6909 (ptp) cc_final: 0.6531 (ptm) REVERT: A 324 HIS cc_start: 0.7676 (t70) cc_final: 0.7245 (t-90) REVERT: B 114 THR cc_start: 0.8369 (t) cc_final: 0.7892 (p) REVERT: B 174 MET cc_start: 0.6923 (ptp) cc_final: 0.6545 (ptm) REVERT: B 324 HIS cc_start: 0.7668 (t70) cc_final: 0.7235 (t-90) REVERT: C 87 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7254 (ppt170) REVERT: C 174 MET cc_start: 0.6860 (ptp) cc_final: 0.6472 (ptm) REVERT: C 324 HIS cc_start: 0.7723 (t70) cc_final: 0.7288 (t-90) REVERT: D 162 LYS cc_start: 0.6530 (pptt) cc_final: 0.5932 (mtmm) REVERT: D 174 MET cc_start: 0.6890 (ptp) cc_final: 0.6512 (ptm) REVERT: D 324 HIS cc_start: 0.7652 (t70) cc_final: 0.7212 (t-90) outliers start: 13 outliers final: 7 residues processed: 159 average time/residue: 2.1185 time to fit residues: 364.2808 Evaluate side-chains 151 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 135 VAL Chi-restraints excluded: chain B residue 176 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 176 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 8 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1655 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= 0.220 Angle : 0.522 4.898 11720 Z= 0.283 Chirality : 0.035 0.127 1260 Planarity : 0.004 0.035 1420 Dihedral : 8.822 65.888 1204 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.61 % Allowed : 29.27 % 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: 2.62 (0.26), residues: 1000 helix: 2.27 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.69 (0.51), 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 0.014 0.001 PHE D 297 TYR 0.010 0.001 TYR D 74 ARG 0.007 0.000 ARG D 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 164 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7229 (ppt170) REVERT: A 114 THR cc_start: 0.8405 (t) cc_final: 0.7953 (p) REVERT: A 174 MET cc_start: 0.6897 (ptp) cc_final: 0.6528 (ptm) REVERT: A 324 HIS cc_start: 0.7641 (t70) cc_final: 0.7212 (t-90) REVERT: B 114 THR cc_start: 0.8391 (t) cc_final: 0.7936 (p) REVERT: B 174 MET cc_start: 0.6920 (ptp) cc_final: 0.6543 (ptm) REVERT: B 324 HIS cc_start: 0.7672 (t70) cc_final: 0.7243 (t-90) REVERT: C 87 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7235 (ppt170) REVERT: C 114 THR cc_start: 0.8371 (t) cc_final: 0.7916 (p) REVERT: C 174 MET cc_start: 0.6897 (ptp) cc_final: 0.6518 (ptm) REVERT: C 324 HIS cc_start: 0.7672 (t70) cc_final: 0.7236 (t-90) REVERT: D 114 THR cc_start: 0.8371 (t) cc_final: 0.7917 (p) REVERT: D 162 LYS cc_start: 0.6537 (pptt) cc_final: 0.5936 (mtmm) REVERT: D 324 HIS cc_start: 0.7658 (t70) cc_final: 0.7220 (t-90) outliers start: 22 outliers final: 13 residues processed: 160 average time/residue: 2.3181 time to fit residues: 397.7923 Evaluate side-chains 154 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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 B residue 207 ARG 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 151 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 176 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8652 Z= 0.198 Angle : 0.522 7.792 11720 Z= 0.281 Chirality : 0.035 0.125 1260 Planarity : 0.004 0.039 1420 Dihedral : 8.731 65.304 1204 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.25 % Allowed : 29.62 % 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: 2.66 (0.26), residues: 1000 helix: 2.29 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.69 (0.52), 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 0.008 0.000 ARG C 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 159 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7226 (ppt170) REVERT: A 114 THR cc_start: 0.8383 (t) cc_final: 0.7928 (p) REVERT: A 123 GLU cc_start: 0.6510 (pp20) cc_final: 0.6270 (pp20) REVERT: A 174 MET cc_start: 0.6894 (ptp) cc_final: 0.6522 (ptm) REVERT: A 324 HIS cc_start: 0.7673 (t70) cc_final: 0.7246 (t-90) REVERT: B 114 THR cc_start: 0.8422 (t) cc_final: 0.7962 (p) REVERT: B 174 MET cc_start: 0.6915 (ptp) cc_final: 0.6538 (ptm) REVERT: B 324 HIS cc_start: 0.7666 (t70) cc_final: 0.7222 (t-90) REVERT: C 87 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7236 (ppt170) REVERT: C 114 THR cc_start: 0.8391 (t) cc_final: 0.7942 (p) REVERT: C 123 GLU cc_start: 0.6657 (pp20) cc_final: 0.6316 (pp20) REVERT: C 174 MET cc_start: 0.6879 (ptp) cc_final: 0.6501 (ptm) REVERT: C 230 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7650 (tmtt) REVERT: C 324 HIS cc_start: 0.7721 (t70) cc_final: 0.7290 (t-90) REVERT: D 114 THR cc_start: 0.8392 (t) cc_final: 0.7943 (p) REVERT: D 123 GLU cc_start: 0.6659 (pp20) cc_final: 0.6317 (pp20) REVERT: D 162 LYS cc_start: 0.6525 (pptt) cc_final: 0.5928 (mtmm) REVERT: D 324 HIS cc_start: 0.7651 (t70) cc_final: 0.7215 (t-90) outliers start: 19 outliers final: 13 residues processed: 154 average time/residue: 2.1670 time to fit residues: 359.7281 Evaluate side-chains 151 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.416 ------------------------------------------------------------------------------- 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 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 207 ARG 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 81 LEU 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 45 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1711 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= 0.198 Angle : 0.509 5.062 11720 Z= 0.274 Chirality : 0.035 0.123 1260 Planarity : 0.004 0.043 1420 Dihedral : 8.660 64.196 1204 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.90 % Allowed : 29.98 % 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: 2.65 (0.26), residues: 1000 helix: 2.29 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.71 (0.52), 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 D 297 TYR 0.009 0.001 TYR D 74 ARG 0.007 0.000 ARG C 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 156 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7218 (ppt170) REVERT: A 114 THR cc_start: 0.8394 (t) cc_final: 0.7936 (p) REVERT: A 116 LYS cc_start: 0.7883 (ttmp) cc_final: 0.7675 (tppp) REVERT: A 123 GLU cc_start: 0.6575 (pp20) cc_final: 0.6358 (pp20) REVERT: A 174 MET cc_start: 0.6894 (ptp) cc_final: 0.6525 (ptm) REVERT: A 324 HIS cc_start: 0.7671 (t70) cc_final: 0.7231 (t-90) REVERT: B 114 THR cc_start: 0.8387 (t) cc_final: 0.7928 (p) REVERT: B 174 MET cc_start: 0.6902 (ptp) cc_final: 0.6520 (ptm) REVERT: B 324 HIS cc_start: 0.7663 (t70) cc_final: 0.7223 (t-90) REVERT: C 87 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7222 (ppt170) REVERT: C 114 THR cc_start: 0.8393 (t) cc_final: 0.7946 (p) REVERT: C 123 GLU cc_start: 0.6675 (pp20) cc_final: 0.6319 (pp20) REVERT: C 174 MET cc_start: 0.6875 (ptp) cc_final: 0.6505 (ptm) REVERT: C 324 HIS cc_start: 0.7674 (t70) cc_final: 0.7228 (t-90) REVERT: D 114 THR cc_start: 0.8394 (t) cc_final: 0.7946 (p) REVERT: D 123 GLU cc_start: 0.6677 (pp20) cc_final: 0.6321 (pp20) REVERT: D 162 LYS cc_start: 0.6497 (pptt) cc_final: 0.5910 (mtmm) REVERT: D 324 HIS cc_start: 0.7649 (t70) cc_final: 0.7216 (t-90) outliers start: 16 outliers final: 13 residues processed: 151 average time/residue: 2.0990 time to fit residues: 342.3630 Evaluate side-chains 153 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 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 113 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 113 SER 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 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 0.0570 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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 = 0.179653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.131484 restraints weight = 79734.329| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.98 r_work: 0.3383 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- 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 = 0.50 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 = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1687 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= 0.163 Angle : 0.493 5.136 11720 Z= 0.266 Chirality : 0.035 0.139 1260 Planarity : 0.003 0.046 1420 Dihedral : 8.492 62.418 1204 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.54 % Allowed : 30.21 % 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: 2.76 (0.26), residues: 1000 helix: 2.37 (0.17), residues: 856 sheet: None (None), residues: 0 loop : -1.67 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 270 HIS 0.001 0.001 HIS D 228 PHE 0.013 0.001 PHE D 297 TYR 0.007 0.001 TYR D 74 ARG 0.009 0.000 ARG C 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6898.53 seconds wall clock time: 122 minutes 32.88 seconds (7352.88 seconds total)