Starting phenix.real_space_refine on Sun Mar 10 14:45:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az4_15753/03_2024/8az4_15753_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az4_15753/03_2024/8az4_15753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az4_15753/03_2024/8az4_15753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az4_15753/03_2024/8az4_15753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az4_15753/03_2024/8az4_15753_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az4_15753/03_2024/8az4_15753_updated.pdb" } resolution = 2.2 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= 0.002 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: 3 Type Number sf(0) Gaussians C 1350 2.51 5 N 420 2.21 5 O 510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2280 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "B" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "C" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "D" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "E" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "F" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "G" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "H" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "I" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "J" Number of atoms: 218 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} Conformer: "B" Number of residues, atoms: 29, 211 Unusual residues: {'NH2': 1} Classifications: {'peptide': 28, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 27} bond proxies already assigned to first conformer: 205 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "J" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 2.43, per 1000 atoms: 1.07 Number of scatterers: 2280 At special positions: 0 Unit cell: (69.3, 72.9, 45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 510 8.00 N 420 7.00 C 1350 6.00 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 - 3.50 Amino acid : False - 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: 0.94 Conformation dependent library (CDL) restraints added in 727.4 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 340 1.28 - 1.35: 410 1.35 - 1.41: 290 1.41 - 1.48: 320 1.48 - 1.54: 870 Bond restraints: 2230 Sorted by residual: bond pdb=" CG ASN E 35 " pdb=" ND2 ASN E 35 " ideal model delta sigma weight residual 1.328 1.312 0.016 2.10e-02 2.27e+03 6.10e-01 bond pdb=" CB ASN D 31 " pdb=" CG ASN D 31 " ideal model delta sigma weight residual 1.516 1.497 0.019 2.50e-02 1.60e+03 6.06e-01 bond pdb=" CD2 TYR C 37 " pdb=" CE2 TYR C 37 " ideal model delta sigma weight residual 1.382 1.359 0.023 3.00e-02 1.11e+03 5.75e-01 bond pdb=" CG1 ILE I 26 " pdb=" CD1 ILE I 26 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.65e-01 bond pdb=" CG ASN F 31 " pdb=" OD1 ASN F 31 " ideal model delta sigma weight residual 1.231 1.217 0.014 1.90e-02 2.77e+03 5.56e-01 ... (remaining 2225 not shown) Histogram of bond angle deviations from ideal: 106.10 - 111.12: 890 111.12 - 116.14: 497 116.14 - 121.17: 979 121.17 - 126.19: 654 126.19 - 131.21: 20 Bond angle restraints: 3040 Sorted by residual: angle pdb=" N THR C 30 " pdb=" CA THR C 30 " pdb=" C THR C 30 " ideal model delta sigma weight residual 109.40 112.94 -3.54 1.63e+00 3.76e-01 4.71e+00 angle pdb=" N THR I 30 " pdb=" CA THR I 30 " pdb=" C THR I 30 " ideal model delta sigma weight residual 109.24 112.77 -3.53 1.67e+00 3.59e-01 4.46e+00 angle pdb=" N THR G 30 " pdb=" CA THR G 30 " pdb=" C THR G 30 " ideal model delta sigma weight residual 109.40 112.77 -3.37 1.63e+00 3.76e-01 4.27e+00 angle pdb=" N THR A 30 " pdb=" CA THR A 30 " pdb=" C THR A 30 " ideal model delta sigma weight residual 109.40 112.76 -3.36 1.63e+00 3.76e-01 4.26e+00 angle pdb=" N SER F 34 " pdb=" CA SER F 34 " pdb=" C SER F 34 " ideal model delta sigma weight residual 111.54 114.31 -2.77 1.36e+00 5.41e-01 4.14e+00 ... (remaining 3035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.77: 1130 10.77 - 21.54: 86 21.54 - 32.31: 29 32.31 - 43.08: 10 43.08 - 53.85: 5 Dihedral angle restraints: 1260 sinusoidal: 440 harmonic: 820 Sorted by residual: dihedral pdb=" CA LEU I 27 " pdb=" CB LEU I 27 " pdb=" CG LEU I 27 " pdb=" CD1 LEU I 27 " ideal model delta sinusoidal sigma weight residual 180.00 146.98 33.02 3 1.50e+01 4.44e-03 5.49e+00 dihedral pdb=" CA LEU E 27 " pdb=" CB LEU E 27 " pdb=" CG LEU E 27 " pdb=" CD1 LEU E 27 " ideal model delta sinusoidal sigma weight residual 180.00 147.02 32.98 3 1.50e+01 4.44e-03 5.48e+00 dihedral pdb=" CA LEU G 27 " pdb=" CB LEU G 27 " pdb=" CG LEU G 27 " pdb=" CD1 LEU G 27 " ideal model delta sinusoidal sigma weight residual 180.00 147.07 32.93 3 1.50e+01 4.44e-03 5.46e+00 ... (remaining 1257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 162 0.031 - 0.062: 114 0.062 - 0.093: 21 0.093 - 0.124: 31 0.124 - 0.155: 12 Chirality restraints: 340 Sorted by residual: chirality pdb=" CA ILE G 26 " pdb=" N ILE G 26 " pdb=" C ILE G 26 " pdb=" CB ILE G 26 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA ILE A 26 " pdb=" N ILE A 26 " pdb=" C ILE A 26 " pdb=" CB ILE A 26 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA ILE H 26 " pdb=" N ILE H 26 " pdb=" C ILE H 26 " pdb=" CB ILE H 26 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 337 not shown) Planarity restraints: 410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU G 27 " -0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C LEU G 27 " 0.020 2.00e-02 2.50e+03 pdb=" O LEU G 27 " -0.008 2.00e-02 2.50e+03 pdb=" N SER G 28 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 29 " -0.005 2.00e-02 2.50e+03 1.08e-02 1.16e+00 pdb=" C SER C 29 " 0.019 2.00e-02 2.50e+03 pdb=" O SER C 29 " -0.007 2.00e-02 2.50e+03 pdb=" N THR C 30 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 27 " -0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C LEU E 27 " 0.018 2.00e-02 2.50e+03 pdb=" O LEU E 27 " -0.007 2.00e-02 2.50e+03 pdb=" N SER E 28 " -0.006 2.00e-02 2.50e+03 ... (remaining 407 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 529 2.81 - 3.34: 1869 3.34 - 3.86: 4316 3.86 - 4.38: 4772 4.38 - 4.90: 8397 Nonbonded interactions: 19883 Sorted by model distance: nonbonded pdb=" OH TYR D 37 " pdb=" O HOH D 101 " model vdw 2.292 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O HOH C 101 " model vdw 2.295 2.440 nonbonded pdb=" OH TYR E 37 " pdb=" O HOH E 101 " model vdw 2.316 2.440 nonbonded pdb=" OH TYR J 37 " pdb=" O HOH J 101 " model vdw 2.322 2.440 nonbonded pdb=" OG SER J 19 " pdb=" O HOH J 102 " model vdw 2.335 2.440 ... (remaining 19878 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'B' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'C' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'D' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'E' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'F' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'G' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'H' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'I' and (resid 10 through 17 or resid 19 through 38)) selection = (chain 'J' and (resid 10 through 17 or resid 19 through 38)) } 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=0.97 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: 0.010 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.810 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.230 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 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 0.029 2230 Z= 0.292 Angle : 0.719 4.752 3040 Z= 0.430 Chirality : 0.053 0.155 340 Planarity : 0.003 0.012 410 Dihedral : 10.223 53.851 740 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: -3.94 (0.28), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.21), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE E 15 TYR 0.010 0.002 TYR E 37 ARG 0.002 0.001 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.260 Fit side-chains REVERT: B 11 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7266 (mmt180) REVERT: I 11 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7553 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 1.2993 time to fit residues: 43.9085 Evaluate side-chains 32 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 2.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A A 21 ASN B 21 ASN C 21 ASN D 18 HIS A D 21 ASN E 18 HIS A E 21 ASN F 18 HIS A F 21 ASN G 18 HIS A G 21 ASN H 21 ASN I 18 HIS A I 21 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2230 Z= 0.132 Angle : 0.595 5.805 3040 Z= 0.304 Chirality : 0.047 0.135 340 Planarity : 0.002 0.011 410 Dihedral : 4.130 10.104 310 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.83 % Allowed : 10.00 % Favored : 89.17 % 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: -3.92 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE H 15 TYR 0.006 0.001 TYR F 37 ARG 0.003 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7516 (mmm-85) REVERT: B 11 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7189 (mmt180) REVERT: D 11 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7219 (mmm-85) REVERT: I 11 ARG cc_start: 0.7768 (mtt180) cc_final: 0.7547 (mtm-85) outliers start: 2 outliers final: 0 residues processed: 33 average time/residue: 1.2851 time to fit residues: 43.4137 Evaluate side-chains 35 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain D residue 11 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 9.9990 chunk 18 optimal weight: 0.1980 chunk 6 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 21 ASN I 21 ASN J 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2230 Z= 0.211 Angle : 0.691 5.843 3040 Z= 0.352 Chirality : 0.050 0.139 340 Planarity : 0.002 0.010 410 Dihedral : 4.196 10.394 310 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.92 % Allowed : 9.17 % Favored : 87.92 % 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: -4.19 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE E 15 TYR 0.010 0.002 TYR I 37 ARG 0.002 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7584 (mmm-85) REVERT: D 11 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7201 (mmm-85) REVERT: G 11 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7154 (mtm-85) REVERT: I 11 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7621 (mtt-85) REVERT: J 11 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7519 (mmm-85) outliers start: 7 outliers final: 1 residues processed: 31 average time/residue: 1.2768 time to fit residues: 40.5447 Evaluate side-chains 35 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain J residue 11 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 10.9990 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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: 0.8520 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2230 Z= 0.253 Angle : 0.728 6.165 3040 Z= 0.375 Chirality : 0.051 0.139 340 Planarity : 0.003 0.008 410 Dihedral : 4.211 10.158 310 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.50 % Allowed : 9.58 % Favored : 87.92 % 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: -4.36 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE E 15 TYR 0.012 0.002 TYR I 37 ARG 0.002 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7638 (mmm-85) REVERT: B 16 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8592 (tt) REVERT: D 11 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7217 (mmm-85) REVERT: G 11 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7137 (mtm-85) REVERT: I 11 ARG cc_start: 0.7830 (mtt180) cc_final: 0.7627 (mtt-85) outliers start: 6 outliers final: 2 residues processed: 32 average time/residue: 1.2837 time to fit residues: 42.0492 Evaluate side-chains 36 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 30 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain J residue 29 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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: 0.8527 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2230 Z= 0.305 Angle : 0.780 6.560 3040 Z= 0.405 Chirality : 0.053 0.142 340 Planarity : 0.003 0.009 410 Dihedral : 4.261 10.315 310 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.92 % Allowed : 9.17 % Favored : 87.92 % 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: -4.41 (0.23), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.17), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE H 15 TYR 0.013 0.002 TYR I 37 ARG 0.002 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7654 (mmm-85) REVERT: D 11 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7225 (mmm-85) REVERT: G 11 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7149 (mtm-85) REVERT: H 16 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8404 (tt) REVERT: I 11 ARG cc_start: 0.7836 (mtt180) cc_final: 0.7632 (mtt-85) REVERT: J 11 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7534 (mmm-85) outliers start: 7 outliers final: 2 residues processed: 32 average time/residue: 1.2324 time to fit residues: 40.4066 Evaluate side-chains 37 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 29 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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: 0.8504 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2230 Z= 0.163 Angle : 0.645 6.841 3040 Z= 0.321 Chirality : 0.048 0.134 340 Planarity : 0.002 0.009 410 Dihedral : 4.133 9.767 310 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.92 % Allowed : 9.58 % Favored : 87.50 % 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: -4.33 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE H 15 TYR 0.008 0.001 TYR I 37 ARG 0.001 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 ARG cc_start: 0.7495 (mtt180) cc_final: 0.7142 (mmt180) REVERT: B 16 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8572 (tt) REVERT: D 11 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7241 (mmm-85) REVERT: G 11 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7128 (mtm-85) REVERT: H 16 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8364 (tt) REVERT: J 11 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7567 (mmm-85) outliers start: 7 outliers final: 1 residues processed: 32 average time/residue: 1.3929 time to fit residues: 45.5565 Evaluate side-chains 37 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 29 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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: 0.8513 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2230 Z= 0.195 Angle : 0.687 7.200 3040 Z= 0.342 Chirality : 0.049 0.136 340 Planarity : 0.002 0.014 410 Dihedral : 4.155 9.808 310 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.33 % Allowed : 10.00 % Favored : 86.67 % 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: -4.33 (0.24), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.18), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE E 15 TYR 0.010 0.001 TYR I 37 ARG 0.003 0.001 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6952 (mmt180) REVERT: B 16 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8577 (tt) REVERT: D 11 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7212 (mmm-85) REVERT: G 11 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7133 (mtm-85) REVERT: H 16 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8364 (tt) REVERT: J 11 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7561 (mmm-85) outliers start: 8 outliers final: 2 residues processed: 32 average time/residue: 1.2522 time to fit residues: 41.0610 Evaluate side-chains 38 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Chi-restraints excluded: chain J residue 29 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 18 HIS A Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.008 2230 Z= 0.099 Angle : 0.597 7.299 3040 Z= 0.280 Chirality : 0.046 0.131 340 Planarity : 0.001 0.009 410 Dihedral : 4.002 9.560 310 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.92 % Allowed : 10.42 % Favored : 86.67 % 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: -4.20 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE E 15 TYR 0.005 0.001 TYR I 37 ARG 0.002 0.000 ARG I 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6934 (mmt-90) REVERT: B 11 ARG cc_start: 0.7494 (mtt180) cc_final: 0.7156 (mmt180) REVERT: B 16 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8528 (tt) REVERT: D 11 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7269 (mmm-85) REVERT: G 11 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7119 (mtm-85) REVERT: H 16 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8332 (tt) REVERT: J 11 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7353 (mtm-85) outliers start: 7 outliers final: 1 residues processed: 31 average time/residue: 1.3650 time to fit residues: 43.2870 Evaluate side-chains 37 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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: 0.8501 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2230 Z= 0.154 Angle : 0.654 7.508 3040 Z= 0.314 Chirality : 0.047 0.133 340 Planarity : 0.002 0.008 410 Dihedral : 4.082 9.345 310 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.92 % Allowed : 10.42 % Favored : 86.67 % 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: -4.27 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE E 15 TYR 0.008 0.001 TYR I 37 ARG 0.001 0.000 ARG C 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6920 (mmt-90) REVERT: B 11 ARG cc_start: 0.7504 (mtt180) cc_final: 0.7152 (mmt180) REVERT: B 16 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8546 (tt) REVERT: D 11 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7215 (mmm-85) REVERT: G 11 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7136 (mtm-85) REVERT: H 16 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8349 (tt) REVERT: J 11 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7535 (mmm-85) outliers start: 7 outliers final: 1 residues processed: 32 average time/residue: 1.3207 time to fit residues: 43.2675 Evaluate side-chains 38 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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: 0.8499 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2230 Z= 0.154 Angle : 0.665 7.565 3040 Z= 0.320 Chirality : 0.048 0.133 340 Planarity : 0.002 0.007 410 Dihedral : 4.083 9.406 310 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.92 % Allowed : 10.42 % Favored : 86.67 % 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: -4.29 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE E 15 TYR 0.007 0.001 TYR I 37 ARG 0.002 0.000 ARG C 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6912 (mmt180) REVERT: B 11 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7155 (mmt180) REVERT: B 16 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8546 (tt) REVERT: D 11 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7230 (mmm-85) REVERT: G 11 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7131 (mtm-85) REVERT: H 16 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8349 (tt) REVERT: J 11 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7546 (mmm-85) outliers start: 7 outliers final: 1 residues processed: 33 average time/residue: 1.3431 time to fit residues: 45.3526 Evaluate side-chains 39 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ARG Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain D residue 11 ARG Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain J residue 11 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 9.9990 chunk 18 optimal weight: 0.0770 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 21 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.098002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.071109 restraints weight = 16567.358| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.92 r_work: 0.3049 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 2230 Z= 0.176 Angle : 0.680 7.585 3040 Z= 0.330 Chirality : 0.048 0.134 340 Planarity : 0.002 0.011 410 Dihedral : 4.106 9.515 310 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.92 % Allowed : 10.42 % Favored : 86.67 % 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: -4.28 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE E 15 TYR 0.008 0.001 TYR I 37 ARG 0.001 0.000 ARG C 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1401.76 seconds wall clock time: 26 minutes 9.41 seconds (1569.41 seconds total)