Starting phenix.real_space_refine on Sun Mar 10 17:09:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az6_15755/03_2024/8az6_15755_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az6_15755/03_2024/8az6_15755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az6_15755/03_2024/8az6_15755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az6_15755/03_2024/8az6_15755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az6_15755/03_2024/8az6_15755_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az6_15755/03_2024/8az6_15755_updated.pdb" } resolution = 3.1 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 2090 2.51 5 N 630 2.21 5 O 700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 11": "NH1" <-> "NH2" 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 ARG 11": "NH1" <-> "NH2" 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 TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 11": "NH1" <-> "NH2" 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 ARG 11": "NH1" <-> "NH2" 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 TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 11": "NH1" <-> "NH2" 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 ARG 11": "NH1" <-> "NH2" Residue "J PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 11": "NH1" <-> "NH2" Residue "N PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 11": "NH1" <-> "NH2" Residue "Q PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 11": "NH1" <-> "NH2" Residue "R PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T 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: 3420 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "B" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "C" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 124 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "D" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 124 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "E" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "F" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "G" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 124 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "H" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 124 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "I" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "J" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "K" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 124 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "L" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 124 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "M" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "N" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "O" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 124 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "P" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 124 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "Q" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "R" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 218 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "S" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 124 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "T" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 124 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Time building chain proxies: 2.16, per 1000 atoms: 0.63 Number of scatterers: 3420 At special positions: 0 Unit cell: (73.8, 90.9, 52.2, 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 700 8.00 N 630 7.00 C 2090 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: 1.22 Conformation dependent library (CDL) restraints added in 533.2 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 820 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: 0.46 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: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 560 1.29 - 1.35: 610 1.35 - 1.42: 416 1.42 - 1.48: 524 1.48 - 1.54: 1350 Bond restraints: 3460 Sorted by residual: bond pdb=" CA ASN E 14 " pdb=" CB ASN E 14 " ideal model delta sigma weight residual 1.534 1.522 0.013 2.47e-02 1.64e+03 2.74e-01 bond pdb=" CA ASN F 14 " pdb=" CB ASN F 14 " ideal model delta sigma weight residual 1.534 1.522 0.013 2.47e-02 1.64e+03 2.65e-01 bond pdb=" CA ASN B 14 " pdb=" CB ASN B 14 " ideal model delta sigma weight residual 1.534 1.522 0.013 2.47e-02 1.64e+03 2.62e-01 bond pdb=" CA ASN A 14 " pdb=" CB ASN A 14 " ideal model delta sigma weight residual 1.534 1.522 0.013 2.47e-02 1.64e+03 2.57e-01 bond pdb=" CA ASN I 14 " pdb=" CB ASN I 14 " ideal model delta sigma weight residual 1.534 1.522 0.012 2.47e-02 1.64e+03 2.43e-01 ... (remaining 3455 not shown) Histogram of bond angle deviations from ideal: 106.10 - 111.12: 1456 111.12 - 116.14: 671 116.14 - 121.16: 1478 121.16 - 126.18: 1085 126.18 - 131.21: 10 Bond angle restraints: 4700 Sorted by residual: angle pdb=" NE ARG R 11 " pdb=" CZ ARG R 11 " pdb=" NH1 ARG R 11 " ideal model delta sigma weight residual 121.50 120.12 1.38 1.00e+00 1.00e+00 1.92e+00 angle pdb=" NE ARG N 11 " pdb=" CZ ARG N 11 " pdb=" NH1 ARG N 11 " ideal model delta sigma weight residual 121.50 120.14 1.36 1.00e+00 1.00e+00 1.86e+00 angle pdb=" NE ARG M 11 " pdb=" CZ ARG M 11 " pdb=" NH1 ARG M 11 " ideal model delta sigma weight residual 121.50 120.14 1.36 1.00e+00 1.00e+00 1.85e+00 angle pdb=" NE ARG B 11 " pdb=" CZ ARG B 11 " pdb=" NH1 ARG B 11 " ideal model delta sigma weight residual 121.50 120.14 1.36 1.00e+00 1.00e+00 1.84e+00 angle pdb=" NE ARG J 11 " pdb=" CZ ARG J 11 " pdb=" NH1 ARG J 11 " ideal model delta sigma weight residual 121.50 120.16 1.34 1.00e+00 1.00e+00 1.80e+00 ... (remaining 4695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.92: 1744 9.92 - 19.83: 121 19.83 - 29.75: 35 29.75 - 39.66: 20 39.66 - 49.58: 10 Dihedral angle restraints: 1930 sinusoidal: 650 harmonic: 1280 Sorted by residual: dihedral pdb=" CA ASN H 22 " pdb=" C ASN H 22 " pdb=" N PHE H 23 " pdb=" CA PHE H 23 " ideal model delta harmonic sigma weight residual 180.00 169.18 10.82 0 5.00e+00 4.00e-02 4.69e+00 dihedral pdb=" CA ASN L 22 " pdb=" C ASN L 22 " pdb=" N PHE L 23 " pdb=" CA PHE L 23 " ideal model delta harmonic sigma weight residual 180.00 169.19 10.81 0 5.00e+00 4.00e-02 4.67e+00 dihedral pdb=" CA ASN K 22 " pdb=" C ASN K 22 " pdb=" N PHE K 23 " pdb=" CA PHE K 23 " ideal model delta harmonic sigma weight residual 180.00 169.22 10.78 0 5.00e+00 4.00e-02 4.65e+00 ... (remaining 1927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 341 0.028 - 0.057: 130 0.057 - 0.085: 29 0.085 - 0.113: 29 0.113 - 0.142: 21 Chirality restraints: 550 Sorted by residual: chirality pdb=" CA ILE O 26 " pdb=" N ILE O 26 " pdb=" C ILE O 26 " pdb=" CB ILE O 26 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE P 26 " pdb=" N ILE P 26 " pdb=" C ILE P 26 " pdb=" CB ILE P 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE R 26 " pdb=" N ILE R 26 " pdb=" C ILE R 26 " pdb=" CB ILE R 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 547 not shown) Planarity restraints: 630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY P 33 " 0.003 2.00e-02 2.50e+03 5.38e-03 2.90e-01 pdb=" C GLY P 33 " -0.009 2.00e-02 2.50e+03 pdb=" O GLY P 33 " 0.004 2.00e-02 2.50e+03 pdb=" N SER P 34 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY O 33 " -0.002 2.00e-02 2.50e+03 4.79e-03 2.29e-01 pdb=" C GLY O 33 " 0.008 2.00e-02 2.50e+03 pdb=" O GLY O 33 " -0.003 2.00e-02 2.50e+03 pdb=" N SER O 34 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS N 18 " 0.004 2.00e-02 2.50e+03 3.78e-03 2.14e-01 pdb=" CG HIS N 18 " -0.008 2.00e-02 2.50e+03 pdb=" ND1 HIS N 18 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS N 18 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS N 18 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS N 18 " 0.002 2.00e-02 2.50e+03 ... (remaining 627 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 184 2.75 - 3.29: 3041 3.29 - 3.82: 6031 3.82 - 4.36: 6411 4.36 - 4.90: 12188 Nonbonded interactions: 27855 Sorted by model distance: nonbonded pdb=" OD1 ASN B 21 " pdb=" ND2 ASN D 35 " model vdw 2.212 2.520 nonbonded pdb=" OD1 ASN R 21 " pdb=" ND2 ASN T 35 " model vdw 2.292 2.520 nonbonded pdb=" OD1 ASN E 21 " pdb=" ND2 ASN G 35 " model vdw 2.296 2.520 nonbonded pdb=" OD1 ASN Q 21 " pdb=" ND2 ASN S 35 " model vdw 2.296 2.520 nonbonded pdb=" OD1 ASN N 21 " pdb=" ND2 ASN P 35 " model vdw 2.301 2.520 ... (remaining 27850 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' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.000 Extract box with map and model: 5.400 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.530 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.004 0.014 3460 Z= 0.173 Angle : 0.428 2.730 4700 Z= 0.249 Chirality : 0.043 0.142 550 Planarity : 0.002 0.005 630 Dihedral : 9.460 49.579 1110 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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: -4.04 (0.19), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.14), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS N 18 PHE 0.004 0.001 PHE L 23 TYR 0.005 0.001 TYR M 37 ARG 0.002 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7354 (mtt180) cc_final: 0.7036 (mmp-170) REVERT: B 11 ARG cc_start: 0.7317 (mtt180) cc_final: 0.6790 (mmp-170) REVERT: P 23 PHE cc_start: 0.7101 (m-80) cc_final: 0.6748 (m-80) REVERT: Q 11 ARG cc_start: 0.7631 (mtt180) cc_final: 0.7368 (ptt90) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1816 time to fit residues: 21.1655 Evaluate side-chains 65 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 ASN D 31 ASN G 31 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN K 31 ASN L 31 ASN O 31 ASN ** O 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 21 ASN P 31 ASN R 10 GLN S 31 ASN T 31 ASN ** T 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3460 Z= 0.191 Angle : 0.496 7.193 4700 Z= 0.256 Chirality : 0.043 0.127 550 Planarity : 0.002 0.006 630 Dihedral : 4.706 16.304 470 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.42 % Allowed : 8.16 % Favored : 88.42 % 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: -4.22 (0.18), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.14), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS J 18 PHE 0.011 0.002 PHE F 15 TYR 0.002 0.001 TYR I 37 ARG 0.001 0.000 ARG Q 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.399 Fit side-chains REVERT: A 11 ARG cc_start: 0.7351 (mtt180) cc_final: 0.7135 (mmp-170) REVERT: B 11 ARG cc_start: 0.7321 (mtt180) cc_final: 0.6783 (mmp-170) REVERT: D 35 ASN cc_start: 0.8781 (t0) cc_final: 0.8458 (t0) REVERT: Q 11 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7300 (ptt90) outliers start: 13 outliers final: 12 residues processed: 92 average time/residue: 0.1803 time to fit residues: 19.5859 Evaluate side-chains 79 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain T residue 32 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 ASN L 35 ASN O 21 ASN ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 3460 Z= 0.143 Angle : 0.481 7.695 4700 Z= 0.237 Chirality : 0.042 0.125 550 Planarity : 0.001 0.005 630 Dihedral : 4.500 16.933 470 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.95 % Allowed : 12.63 % Favored : 83.42 % 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: -4.39 (0.18), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.14), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Q 18 PHE 0.010 0.001 PHE O 23 TYR 0.002 0.001 TYR D 37 ARG 0.001 0.000 ARG M 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.403 Fit side-chains REVERT: A 11 ARG cc_start: 0.7332 (mtt180) cc_final: 0.7092 (mmp-170) REVERT: B 11 ARG cc_start: 0.7373 (mtt180) cc_final: 0.6966 (mmp-170) REVERT: I 10 GLN cc_start: 0.7887 (tt0) cc_final: 0.7600 (tt0) REVERT: L 31 ASN cc_start: 0.8583 (t0) cc_final: 0.8358 (t0) REVERT: Q 11 ARG cc_start: 0.7671 (mtt180) cc_final: 0.7322 (ptt90) outliers start: 15 outliers final: 14 residues processed: 89 average time/residue: 0.1967 time to fit residues: 20.7053 Evaluate side-chains 85 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 32 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN J 14 ASN O 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 3460 Z= 0.239 Angle : 0.532 6.852 4700 Z= 0.269 Chirality : 0.043 0.128 550 Planarity : 0.002 0.009 630 Dihedral : 4.822 16.339 470 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.00 % Allowed : 13.42 % Favored : 81.58 % 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: -4.66 (0.18), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.14), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 18 PHE 0.011 0.002 PHE T 23 TYR 0.003 0.001 TYR N 37 ARG 0.002 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.397 Fit side-chains REVERT: B 11 ARG cc_start: 0.7372 (mtt180) cc_final: 0.7002 (mmp-170) REVERT: I 10 GLN cc_start: 0.7875 (tt0) cc_final: 0.7588 (tt0) REVERT: L 31 ASN cc_start: 0.8576 (t0) cc_final: 0.8347 (t0) outliers start: 19 outliers final: 19 residues processed: 88 average time/residue: 0.1834 time to fit residues: 18.9925 Evaluate side-chains 87 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain S residue 30 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN O 21 ASN S 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.024 3460 Z= 0.319 Angle : 0.573 7.520 4700 Z= 0.296 Chirality : 0.045 0.127 550 Planarity : 0.002 0.010 630 Dihedral : 5.030 17.137 470 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 6.05 % Allowed : 15.53 % Favored : 78.42 % 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: -5.01 (0.18), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.13), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 18 PHE 0.010 0.002 PHE A 15 TYR 0.004 0.001 TYR N 37 ARG 0.001 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 66 time to evaluate : 0.405 Fit side-chains REVERT: A 11 ARG cc_start: 0.7595 (mtm180) cc_final: 0.7348 (mmp-170) REVERT: B 11 ARG cc_start: 0.7370 (mtt180) cc_final: 0.7071 (mmp-170) REVERT: I 10 GLN cc_start: 0.7866 (tt0) cc_final: 0.7526 (tt0) REVERT: L 31 ASN cc_start: 0.8624 (t0) cc_final: 0.8389 (t0) outliers start: 23 outliers final: 23 residues processed: 83 average time/residue: 0.1945 time to fit residues: 18.9362 Evaluate side-chains 89 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 66 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 32 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN S 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.015 3460 Z= 0.071 Angle : 0.470 8.523 4700 Z= 0.221 Chirality : 0.043 0.123 550 Planarity : 0.001 0.004 630 Dihedral : 3.918 13.767 470 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.84 % Allowed : 19.47 % Favored : 78.68 % 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: -4.93 (0.20), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 18 PHE 0.006 0.001 PHE P 23 TYR 0.005 0.001 TYR O 37 ARG 0.000 0.000 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.378 Fit side-chains REVERT: A 11 ARG cc_start: 0.7506 (mtm180) cc_final: 0.7230 (mmp-170) REVERT: B 11 ARG cc_start: 0.7429 (mtt180) cc_final: 0.7056 (mmp-170) REVERT: I 10 GLN cc_start: 0.7752 (tt0) cc_final: 0.7516 (tt0) outliers start: 7 outliers final: 6 residues processed: 77 average time/residue: 0.2082 time to fit residues: 18.7201 Evaluate side-chains 69 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 32 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 ASN F 18 HIS H 31 ASN J 18 HIS K 31 ASN M 18 HIS O 31 ASN P 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 3460 Z= 0.223 Angle : 0.525 8.212 4700 Z= 0.264 Chirality : 0.043 0.125 550 Planarity : 0.002 0.009 630 Dihedral : 4.521 13.980 470 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.47 % Allowed : 18.68 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.06 (0.20), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.15), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 18 PHE 0.010 0.002 PHE G 23 TYR 0.003 0.001 TYR N 37 ARG 0.001 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.377 Fit side-chains REVERT: A 11 ARG cc_start: 0.7569 (mtm180) cc_final: 0.7222 (mmp-170) REVERT: B 11 ARG cc_start: 0.7326 (mtt180) cc_final: 0.7109 (mmp-170) REVERT: I 10 GLN cc_start: 0.7795 (tt0) cc_final: 0.7496 (tt0) outliers start: 17 outliers final: 17 residues processed: 77 average time/residue: 0.2076 time to fit residues: 18.7331 Evaluate side-chains 77 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 32 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 5.9990 chunk 30 optimal weight: 0.0040 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 0.1980 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3460 Z= 0.108 Angle : 0.483 8.474 4700 Z= 0.233 Chirality : 0.043 0.124 550 Planarity : 0.001 0.006 630 Dihedral : 4.084 12.727 470 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.84 % Allowed : 20.53 % Favored : 77.63 % 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: -5.03 (0.22), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 18 PHE 0.007 0.001 PHE P 23 TYR 0.003 0.001 TYR L 37 ARG 0.001 0.000 ARG R 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.365 Fit side-chains REVERT: A 11 ARG cc_start: 0.7544 (mtm180) cc_final: 0.7209 (mmp-170) REVERT: B 11 ARG cc_start: 0.7384 (mtt180) cc_final: 0.7100 (mmp-170) REVERT: I 10 GLN cc_start: 0.7752 (tt0) cc_final: 0.7465 (tt0) outliers start: 7 outliers final: 7 residues processed: 69 average time/residue: 0.2079 time to fit residues: 16.7158 Evaluate side-chains 68 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 32 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 36 optimal weight: 0.3980 chunk 31 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS P 31 ASN Q 18 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.024 3460 Z= 0.262 Angle : 0.545 7.988 4700 Z= 0.277 Chirality : 0.044 0.128 550 Planarity : 0.002 0.008 630 Dihedral : 4.587 14.649 470 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.21 % Allowed : 18.95 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.15 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 18 PHE 0.012 0.002 PHE T 23 TYR 0.003 0.001 TYR N 37 ARG 0.001 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.396 Fit side-chains REVERT: A 11 ARG cc_start: 0.7591 (mtm180) cc_final: 0.7233 (mmp-170) REVERT: B 11 ARG cc_start: 0.7355 (mtt180) cc_final: 0.7117 (mmp-170) REVERT: I 10 GLN cc_start: 0.7856 (tt0) cc_final: 0.7595 (tt0) outliers start: 16 outliers final: 16 residues processed: 71 average time/residue: 0.2199 time to fit residues: 18.2113 Evaluate side-chains 71 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 32 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 4 optimal weight: 0.0670 chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- 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: 0.8294 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3460 Z= 0.199 Angle : 0.529 8.141 4700 Z= 0.263 Chirality : 0.043 0.127 550 Planarity : 0.002 0.007 630 Dihedral : 4.479 14.429 470 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.68 % Allowed : 19.74 % Favored : 76.58 % 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: -5.23 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 18 PHE 0.010 0.002 PHE P 23 TYR 0.002 0.001 TYR N 37 ARG 0.001 0.000 ARG A 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.366 Fit side-chains REVERT: A 11 ARG cc_start: 0.7576 (mtm180) cc_final: 0.7212 (mmp-170) REVERT: B 11 ARG cc_start: 0.7383 (mtt180) cc_final: 0.7162 (mmp-170) REVERT: I 10 GLN cc_start: 0.7793 (tt0) cc_final: 0.7540 (tt0) outliers start: 14 outliers final: 14 residues processed: 74 average time/residue: 0.2198 time to fit residues: 19.0289 Evaluate side-chains 70 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 32 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.123286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.085107 restraints weight = 4337.218| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.19 r_work: 0.3223 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 3460 Z= 0.271 Angle : 0.563 8.055 4700 Z= 0.285 Chirality : 0.045 0.128 550 Planarity : 0.002 0.010 630 Dihedral : 4.657 15.077 470 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.47 % Allowed : 19.21 % Favored : 76.32 % 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: -5.33 (0.20), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.05 (0.15), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS R 18 PHE 0.012 0.002 PHE P 23 TYR 0.003 0.001 TYR N 37 ARG 0.001 0.000 ARG A 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1261.31 seconds wall clock time: 23 minutes 12.61 seconds (1392.61 seconds total)