Starting phenix.real_space_refine on Fri Jul 19 09:20:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/07_2024/8t03_40933_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/07_2024/8t03_40933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/07_2024/8t03_40933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/07_2024/8t03_40933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/07_2024/8t03_40933_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t03_40933/07_2024/8t03_40933_neut.cif" } resolution = 2.72 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= 0.002 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 44 5.16 5 C 4492 2.51 5 N 1092 2.21 5 O 1246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 87": "OD1" <-> "OD2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "D PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "F PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6878 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1593 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "B" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1593 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain: "C" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 936 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {' ZN': 1, 'CLR': 1, 'LBN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.90, per 1000 atoms: 0.71 Number of scatterers: 6878 At special positions: 0 Unit cell: (92.13, 103.75, 103.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 44 16.00 P 2 15.00 O 1246 8.00 N 1092 7.00 C 4492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 59 " distance=2.04 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 59 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 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: 2.63 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 184 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 180 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 48 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 184 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 180 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 48 " 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 12 sheets defined 41.0% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 removed outlier: 3.975A pdb=" N LEU A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Proline residue: A 11 - end of helix Processing helix chain 'A' and resid 18 through 28 Processing helix chain 'A' and resid 30 through 52 Processing helix chain 'A' and resid 62 through 87 Processing helix chain 'A' and resid 91 through 111 Processing helix chain 'A' and resid 118 through 141 Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 153 through 170 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 176 through 195 removed outlier: 3.704A pdb=" N SER A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 15 Proline residue: B 11 - end of helix Processing helix chain 'B' and resid 18 through 28 Processing helix chain 'B' and resid 30 through 52 Processing helix chain 'B' and resid 62 through 87 Processing helix chain 'B' and resid 91 through 111 Processing helix chain 'B' and resid 118 through 141 Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 153 through 170 Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 176 through 195 removed outlier: 3.704A pdb=" N SER B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.516A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.515A pdb=" N ILE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.597A pdb=" N LEU C 12 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL C 36 " --> pdb=" O HIS C 52 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N HIS C 52 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP C 38 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.597A pdb=" N LEU C 12 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR C 109 " --> pdb=" O ARG C 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.419A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE D 33 " --> pdb=" O HIS D 49 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N HIS D 49 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.419A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.598A pdb=" N LEU E 12 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL E 36 " --> pdb=" O HIS E 52 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N HIS E 52 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP E 38 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.598A pdb=" N LEU E 12 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR E 109 " --> pdb=" O ARG E 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.418A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE F 33 " --> pdb=" O HIS F 49 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N HIS F 49 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.418A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1145 1.33 - 1.45: 1929 1.45 - 1.57: 3908 1.57 - 1.69: 4 1.69 - 1.82: 72 Bond restraints: 7058 Sorted by residual: bond pdb=" N LEU A 55 " pdb=" CA LEU A 55 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.00e-02 1.00e+04 1.37e+01 bond pdb=" N LEU B 55 " pdb=" CA LEU B 55 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.00e-02 1.00e+04 1.33e+01 bond pdb=" N LEU B 10 " pdb=" CA LEU B 10 " ideal model delta sigma weight residual 1.461 1.495 -0.034 9.20e-03 1.18e+04 1.33e+01 bond pdb=" N LEU A 10 " pdb=" CA LEU A 10 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.20e-03 1.18e+04 1.28e+01 bond pdb=" N ARG E 68 " pdb=" CA ARG E 68 " ideal model delta sigma weight residual 1.454 1.504 -0.050 1.42e-02 4.96e+03 1.24e+01 ... (remaining 7053 not shown) Histogram of bond angle deviations from ideal: 94.81 - 102.87: 50 102.87 - 110.93: 2064 110.93 - 118.98: 4328 118.98 - 127.04: 3029 127.04 - 135.10: 93 Bond angle restraints: 9564 Sorted by residual: angle pdb=" C PHE E 54 " pdb=" N TRP E 55 " pdb=" CA TRP E 55 " ideal model delta sigma weight residual 120.38 127.50 -7.12 1.37e+00 5.33e-01 2.70e+01 angle pdb=" C PHE C 54 " pdb=" N TRP C 55 " pdb=" CA TRP C 55 " ideal model delta sigma weight residual 120.38 127.48 -7.10 1.37e+00 5.33e-01 2.68e+01 angle pdb=" CA GLY C 113 " pdb=" C GLY C 113 " pdb=" O GLY C 113 " ideal model delta sigma weight residual 122.24 117.94 4.30 8.70e-01 1.32e+00 2.44e+01 angle pdb=" CA GLY E 113 " pdb=" C GLY E 113 " pdb=" O GLY E 113 " ideal model delta sigma weight residual 122.24 117.97 4.27 8.70e-01 1.32e+00 2.41e+01 angle pdb=" CA GLY D 101 " pdb=" C GLY D 101 " pdb=" O GLY D 101 " ideal model delta sigma weight residual 122.29 118.46 3.83 8.10e-01 1.52e+00 2.24e+01 ... (remaining 9559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 4124 35.87 - 71.74: 116 71.74 - 107.61: 4 107.61 - 143.48: 2 143.48 - 179.35: 4 Dihedral angle restraints: 4250 sinusoidal: 1788 harmonic: 2462 Sorted by residual: dihedral pdb=" CA GLU A 90 " pdb=" C GLU A 90 " pdb=" N PRO A 91 " pdb=" CA PRO A 91 " ideal model delta harmonic sigma weight residual 0.00 38.51 -38.51 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CA GLU B 90 " pdb=" C GLU B 90 " pdb=" N PRO B 91 " pdb=" CA PRO B 91 " ideal model delta harmonic sigma weight residual 0.00 38.43 -38.43 0 5.00e+00 4.00e-02 5.91e+01 dihedral pdb=" C1 LBN B 303 " pdb=" O1 LBN B 303 " pdb=" P1 LBN B 303 " pdb=" O3 LBN B 303 " ideal model delta sinusoidal sigma weight residual 275.40 96.05 179.35 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.970: 1052 0.970 - 1.939: 0 1.939 - 2.909: 0 2.909 - 3.879: 0 3.879 - 4.848: 2 Chirality restraints: 1054 Sorted by residual: chirality pdb=" C2 LBN B 303 " pdb=" C1 LBN B 303 " pdb=" C3 LBN B 303 " pdb=" O7 LBN B 303 " both_signs ideal model delta sigma weight residual False -2.36 2.48 -4.85 2.00e-01 2.50e+01 5.88e+02 chirality pdb=" C2 LBN A 303 " pdb=" C1 LBN A 303 " pdb=" C3 LBN A 303 " pdb=" O7 LBN A 303 " both_signs ideal model delta sigma weight residual False -2.36 2.48 -4.85 2.00e-01 2.50e+01 5.87e+02 chirality pdb=" CA ILE D 75 " pdb=" N ILE D 75 " pdb=" C ILE D 75 " pdb=" CB ILE D 75 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1051 not shown) Planarity restraints: 1156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN B 303 " -0.038 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C42 LBN B 303 " 0.038 2.00e-02 2.50e+03 pdb=" C5 LBN B 303 " 0.039 2.00e-02 2.50e+03 pdb=" C8 LBN B 303 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN A 303 " 0.038 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C42 LBN A 303 " -0.038 2.00e-02 2.50e+03 pdb=" C5 LBN A 303 " -0.039 2.00e-02 2.50e+03 pdb=" C8 LBN A 303 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 90 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO A 91 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " 0.026 5.00e-02 4.00e+02 ... (remaining 1153 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 349 2.74 - 3.28: 6600 3.28 - 3.82: 10749 3.82 - 4.36: 14874 4.36 - 4.90: 24913 Nonbonded interactions: 57485 Sorted by model distance: nonbonded pdb=" OD1 ASP D 28 " pdb=" O GLY D 68 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASP F 28 " pdb=" O GLY F 68 " model vdw 2.206 3.040 nonbonded pdb=" CE1 TYR D 86 " pdb=" CD1 LEU D 104 " model vdw 2.395 3.760 nonbonded pdb=" CE1 TYR F 86 " pdb=" CD1 LEU F 104 " model vdw 2.397 3.760 nonbonded pdb=" NH2 ARG F 61 " pdb=" OE1 GLU F 79 " model vdw 2.430 2.520 ... (remaining 57480 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' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 1.490 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.980 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 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 : 0.014 0.050 7058 Z= 0.887 Angle : 1.758 11.254 9564 Z= 1.287 Chirality : 0.227 4.848 1054 Planarity : 0.004 0.051 1156 Dihedral : 17.024 179.354 2666 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.63 % Allowed : 4.90 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -0.46 (0.29), residues: 840 helix: -0.62 (0.26), residues: 294 sheet: 0.45 (0.39), residues: 196 loop : -0.27 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 110 HIS 0.008 0.002 HIS B 110 PHE 0.022 0.003 PHE A 46 TYR 0.027 0.003 TYR F 71 ARG 0.003 0.001 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 0.698 Fit side-chains REVERT: A 29 ARG cc_start: 0.7286 (mmm160) cc_final: 0.7076 (mtp180) REVERT: A 61 MET cc_start: 0.7701 (mtm) cc_final: 0.7328 (mtp) REVERT: A 134 LEU cc_start: 0.7325 (mt) cc_final: 0.7024 (mm) REVERT: A 138 LYS cc_start: 0.6890 (mptt) cc_final: 0.6518 (mptt) REVERT: A 139 GLU cc_start: 0.6813 (tt0) cc_final: 0.6456 (tt0) REVERT: B 29 ARG cc_start: 0.7294 (mmm160) cc_final: 0.7089 (mtp180) REVERT: B 61 MET cc_start: 0.7670 (mtm) cc_final: 0.7319 (mtp) REVERT: B 134 LEU cc_start: 0.7320 (mt) cc_final: 0.7023 (mm) REVERT: B 138 LYS cc_start: 0.6891 (mptt) cc_final: 0.6506 (mptt) REVERT: B 139 GLU cc_start: 0.6827 (tt0) cc_final: 0.6470 (tt0) REVERT: C 41 LYS cc_start: 0.7093 (tttt) cc_final: 0.6753 (ttpp) REVERT: C 61 TYR cc_start: 0.8446 (m-80) cc_final: 0.8099 (m-80) REVERT: C 112 GLN cc_start: 0.7583 (tt0) cc_final: 0.7178 (tt0) REVERT: D 31 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6359 (mp0) REVERT: D 42 LYS cc_start: 0.7527 (mtpp) cc_final: 0.6803 (mtmt) REVERT: E 41 LYS cc_start: 0.7062 (tttt) cc_final: 0.6705 (ttpp) REVERT: E 61 TYR cc_start: 0.8424 (m-80) cc_final: 0.8081 (m-80) REVERT: E 83 MET cc_start: 0.6350 (mmm) cc_final: 0.6123 (mpt) REVERT: F 31 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6297 (mp0) REVERT: F 42 LYS cc_start: 0.7644 (mtpp) cc_final: 0.6966 (mtmt) outliers start: 12 outliers final: 2 residues processed: 134 average time/residue: 1.1519 time to fit residues: 162.9058 Evaluate side-chains 100 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain F residue 61 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 64 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7058 Z= 0.190 Angle : 0.581 6.372 9564 Z= 0.301 Chirality : 0.043 0.143 1054 Planarity : 0.004 0.034 1156 Dihedral : 13.816 154.781 1144 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.45 % Allowed : 9.54 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.99 (0.30), residues: 840 helix: 1.57 (0.28), residues: 304 sheet: 0.68 (0.34), residues: 230 loop : -0.20 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 110 HIS 0.003 0.001 HIS B 184 PHE 0.018 0.002 PHE A 39 TYR 0.012 0.001 TYR F 91 ARG 0.002 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.769 Fit side-chains REVERT: A 27 LYS cc_start: 0.6851 (ttmt) cc_final: 0.6265 (mttt) REVERT: A 134 LEU cc_start: 0.6733 (mt) cc_final: 0.6495 (mm) REVERT: A 138 LYS cc_start: 0.6338 (mptt) cc_final: 0.6107 (mptt) REVERT: A 139 GLU cc_start: 0.6586 (tt0) cc_final: 0.6264 (tt0) REVERT: B 27 LYS cc_start: 0.6853 (ttmt) cc_final: 0.6257 (mttt) REVERT: B 134 LEU cc_start: 0.6744 (mt) cc_final: 0.6509 (mm) REVERT: B 138 LYS cc_start: 0.6366 (mptt) cc_final: 0.6135 (mptt) REVERT: B 139 GLU cc_start: 0.6578 (tt0) cc_final: 0.6213 (tt0) REVERT: C 41 LYS cc_start: 0.7018 (tttt) cc_final: 0.6712 (tttp) REVERT: D 31 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6443 (mp0) REVERT: D 42 LYS cc_start: 0.7304 (mtpp) cc_final: 0.6668 (mtmt) REVERT: D 45 ARG cc_start: 0.7017 (mtm180) cc_final: 0.6628 (mtp180) REVERT: D 55 GLN cc_start: 0.7502 (tp40) cc_final: 0.7300 (tp40) REVERT: E 41 LYS cc_start: 0.7035 (tttt) cc_final: 0.6662 (ttpp) REVERT: E 96 TYR cc_start: 0.7493 (m-80) cc_final: 0.7012 (m-80) REVERT: F 31 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6364 (mp0) REVERT: F 42 LYS cc_start: 0.7298 (mtpp) cc_final: 0.6814 (mtmm) outliers start: 18 outliers final: 5 residues processed: 124 average time/residue: 1.3492 time to fit residues: 175.2674 Evaluate side-chains 116 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 112 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 0.0970 chunk 74 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7058 Z= 0.148 Angle : 0.514 6.190 9564 Z= 0.265 Chirality : 0.041 0.136 1054 Planarity : 0.004 0.032 1156 Dihedral : 12.512 152.418 1136 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.59 % Allowed : 12.40 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.43 (0.29), residues: 840 helix: 2.07 (0.28), residues: 306 sheet: 0.81 (0.34), residues: 240 loop : -0.06 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 110 HIS 0.002 0.001 HIS A 110 PHE 0.015 0.001 PHE A 46 TYR 0.010 0.001 TYR D 91 ARG 0.001 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.759 Fit side-chains REVERT: A 27 LYS cc_start: 0.7141 (ttmt) cc_final: 0.6613 (mttt) REVERT: A 134 LEU cc_start: 0.6710 (mt) cc_final: 0.6492 (mm) REVERT: A 138 LYS cc_start: 0.6347 (mptt) cc_final: 0.6103 (mptt) REVERT: A 139 GLU cc_start: 0.6678 (tt0) cc_final: 0.6367 (tt0) REVERT: B 27 LYS cc_start: 0.7143 (ttmt) cc_final: 0.6612 (mttt) REVERT: B 134 LEU cc_start: 0.6715 (mt) cc_final: 0.6498 (mm) REVERT: B 138 LYS cc_start: 0.6424 (mptt) cc_final: 0.6168 (mptt) REVERT: B 139 GLU cc_start: 0.6677 (tt0) cc_final: 0.6329 (tt0) REVERT: D 31 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6557 (mp0) REVERT: D 42 LYS cc_start: 0.7293 (mtpp) cc_final: 0.6788 (mtpt) REVERT: D 45 ARG cc_start: 0.6901 (mtm180) cc_final: 0.6594 (mtp180) REVERT: F 5 THR cc_start: 0.6665 (m) cc_final: 0.6347 (p) REVERT: F 31 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6465 (mp0) REVERT: F 42 LYS cc_start: 0.7273 (mtpp) cc_final: 0.6774 (mtmm) REVERT: F 61 ARG cc_start: 0.6705 (ptt90) cc_final: 0.6373 (ptp90) outliers start: 19 outliers final: 5 residues processed: 118 average time/residue: 1.3552 time to fit residues: 167.5433 Evaluate side-chains 115 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 0.0170 chunk 21 optimal weight: 0.7980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7058 Z= 0.134 Angle : 0.499 6.170 9564 Z= 0.255 Chirality : 0.040 0.141 1054 Planarity : 0.004 0.040 1156 Dihedral : 11.453 140.484 1136 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.18 % Allowed : 13.49 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.74 (0.30), residues: 840 helix: 2.38 (0.28), residues: 304 sheet: 1.05 (0.34), residues: 240 loop : -0.01 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 110 HIS 0.002 0.001 HIS E 52 PHE 0.014 0.001 PHE B 39 TYR 0.010 0.001 TYR D 86 ARG 0.002 0.000 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.746 Fit side-chains REVERT: A 27 LYS cc_start: 0.7134 (ttmt) cc_final: 0.6568 (mttt) REVERT: A 134 LEU cc_start: 0.6704 (mt) cc_final: 0.6489 (mm) REVERT: A 138 LYS cc_start: 0.6504 (mptt) cc_final: 0.6223 (mptt) REVERT: A 139 GLU cc_start: 0.6706 (tt0) cc_final: 0.6392 (tt0) REVERT: B 27 LYS cc_start: 0.7147 (ttmt) cc_final: 0.6595 (mttt) REVERT: B 103 THR cc_start: 0.8119 (m) cc_final: 0.7766 (p) REVERT: B 134 LEU cc_start: 0.6704 (mt) cc_final: 0.6494 (mm) REVERT: B 138 LYS cc_start: 0.6501 (mptt) cc_final: 0.6217 (mptt) REVERT: B 139 GLU cc_start: 0.6701 (tt0) cc_final: 0.6390 (tt0) REVERT: C 48 GLU cc_start: 0.7109 (tt0) cc_final: 0.6733 (tt0) REVERT: C 114 THR cc_start: 0.7336 (t) cc_final: 0.6949 (p) REVERT: D 5 THR cc_start: 0.6497 (m) cc_final: 0.6274 (p) REVERT: D 31 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6619 (mp0) REVERT: D 42 LYS cc_start: 0.7259 (mtpp) cc_final: 0.6784 (mtpt) REVERT: D 45 ARG cc_start: 0.6855 (mtm180) cc_final: 0.6428 (mtp180) REVERT: E 48 GLU cc_start: 0.7107 (tt0) cc_final: 0.6735 (tt0) REVERT: F 31 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6558 (mp0) REVERT: F 42 LYS cc_start: 0.7258 (mtpp) cc_final: 0.6759 (mtmm) outliers start: 16 outliers final: 9 residues processed: 120 average time/residue: 1.1997 time to fit residues: 151.5879 Evaluate side-chains 117 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 74 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.0570 chunk 44 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN F 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7058 Z= 0.163 Angle : 0.505 6.242 9564 Z= 0.260 Chirality : 0.041 0.142 1054 Planarity : 0.004 0.047 1156 Dihedral : 11.069 134.333 1136 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.59 % Allowed : 13.62 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.85 (0.30), residues: 840 helix: 2.36 (0.28), residues: 304 sheet: 1.23 (0.35), residues: 240 loop : 0.06 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 110 HIS 0.002 0.001 HIS E 52 PHE 0.015 0.001 PHE A 39 TYR 0.011 0.001 TYR F 86 ARG 0.001 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.778 Fit side-chains REVERT: A 27 LYS cc_start: 0.6959 (ttmt) cc_final: 0.6417 (mttt) REVERT: A 134 LEU cc_start: 0.6717 (mt) cc_final: 0.6476 (mm) REVERT: A 138 LYS cc_start: 0.6470 (mptt) cc_final: 0.6184 (mptt) REVERT: A 139 GLU cc_start: 0.6722 (tt0) cc_final: 0.6415 (tt0) REVERT: B 27 LYS cc_start: 0.6958 (ttmt) cc_final: 0.6415 (mttt) REVERT: B 134 LEU cc_start: 0.6720 (mt) cc_final: 0.6485 (mm) REVERT: B 138 LYS cc_start: 0.6600 (mptt) cc_final: 0.6309 (mptt) REVERT: B 139 GLU cc_start: 0.6719 (tt0) cc_final: 0.6412 (tt0) REVERT: C 48 GLU cc_start: 0.7118 (tt0) cc_final: 0.6712 (tt0) REVERT: C 114 THR cc_start: 0.7327 (t) cc_final: 0.6954 (p) REVERT: D 31 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6605 (mp0) REVERT: D 42 LYS cc_start: 0.7245 (mtpp) cc_final: 0.6739 (mtmm) REVERT: D 45 ARG cc_start: 0.6859 (mtm180) cc_final: 0.6396 (mtp180) REVERT: D 61 ARG cc_start: 0.6752 (ptp90) cc_final: 0.6325 (ptp90) REVERT: E 48 GLU cc_start: 0.7104 (tt0) cc_final: 0.6686 (tt0) REVERT: F 31 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6554 (mp0) REVERT: F 42 LYS cc_start: 0.7270 (mtpp) cc_final: 0.6767 (mtmm) outliers start: 19 outliers final: 12 residues processed: 113 average time/residue: 1.2111 time to fit residues: 144.1534 Evaluate side-chains 117 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN F 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7058 Z= 0.185 Angle : 0.519 6.280 9564 Z= 0.267 Chirality : 0.041 0.142 1054 Planarity : 0.005 0.050 1156 Dihedral : 10.836 127.730 1136 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.45 % Allowed : 13.62 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.86 (0.30), residues: 840 helix: 2.30 (0.28), residues: 304 sheet: 1.29 (0.35), residues: 240 loop : 0.12 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 110 HIS 0.003 0.001 HIS F 38 PHE 0.016 0.002 PHE A 69 TYR 0.011 0.001 TYR F 86 ARG 0.002 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 0.798 Fit side-chains REVERT: A 27 LYS cc_start: 0.6954 (ttmt) cc_final: 0.6479 (mttt) REVERT: A 134 LEU cc_start: 0.6716 (mt) cc_final: 0.6465 (mm) REVERT: A 138 LYS cc_start: 0.6637 (mptt) cc_final: 0.6342 (mptt) REVERT: A 139 GLU cc_start: 0.6707 (tt0) cc_final: 0.6354 (tt0) REVERT: B 27 LYS cc_start: 0.6955 (ttmt) cc_final: 0.6479 (mttt) REVERT: B 134 LEU cc_start: 0.6718 (mt) cc_final: 0.6472 (mm) REVERT: B 138 LYS cc_start: 0.6623 (mptt) cc_final: 0.6328 (mptt) REVERT: B 139 GLU cc_start: 0.6641 (tt0) cc_final: 0.6288 (tt0) REVERT: C 48 GLU cc_start: 0.7151 (tt0) cc_final: 0.6703 (tt0) REVERT: C 114 THR cc_start: 0.7332 (t) cc_final: 0.6972 (p) REVERT: D 31 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6612 (mp0) REVERT: D 42 LYS cc_start: 0.7257 (mtpp) cc_final: 0.6764 (mtmm) REVERT: D 45 ARG cc_start: 0.6897 (mtm180) cc_final: 0.6399 (mtp180) REVERT: E 48 GLU cc_start: 0.7187 (tt0) cc_final: 0.6743 (tt0) REVERT: F 31 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6595 (mp0) REVERT: F 42 LYS cc_start: 0.7256 (mtpp) cc_final: 0.6773 (mtmm) outliers start: 18 outliers final: 12 residues processed: 118 average time/residue: 1.2854 time to fit residues: 159.4287 Evaluate side-chains 120 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 74 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN E 16 GLN F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7058 Z= 0.225 Angle : 0.549 6.374 9564 Z= 0.281 Chirality : 0.042 0.151 1054 Planarity : 0.005 0.050 1156 Dihedral : 10.991 131.050 1136 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.59 % Allowed : 13.62 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.74 (0.30), residues: 840 helix: 2.16 (0.27), residues: 304 sheet: 1.22 (0.35), residues: 240 loop : 0.10 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 110 HIS 0.003 0.001 HIS D 38 PHE 0.017 0.002 PHE B 69 TYR 0.013 0.002 TYR F 86 ARG 0.002 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.800 Fit side-chains REVERT: A 27 LYS cc_start: 0.6819 (ttmt) cc_final: 0.6344 (mttt) REVERT: A 134 LEU cc_start: 0.6739 (mt) cc_final: 0.6465 (mm) REVERT: A 138 LYS cc_start: 0.6678 (mptt) cc_final: 0.6367 (mptt) REVERT: A 139 GLU cc_start: 0.6678 (tt0) cc_final: 0.6369 (tt0) REVERT: B 27 LYS cc_start: 0.6823 (ttmt) cc_final: 0.6343 (mttt) REVERT: B 134 LEU cc_start: 0.6726 (mt) cc_final: 0.6456 (mm) REVERT: B 138 LYS cc_start: 0.6542 (mptt) cc_final: 0.6310 (mptt) REVERT: B 139 GLU cc_start: 0.6679 (tt0) cc_final: 0.6370 (tt0) REVERT: C 48 GLU cc_start: 0.7183 (tt0) cc_final: 0.6721 (tt0) REVERT: C 114 THR cc_start: 0.7305 (t) cc_final: 0.6938 (p) REVERT: D 31 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6614 (mp0) REVERT: D 42 LYS cc_start: 0.7278 (mtpp) cc_final: 0.6795 (mtmm) REVERT: D 61 ARG cc_start: 0.6958 (ptp90) cc_final: 0.6674 (ptp90) REVERT: E 48 GLU cc_start: 0.7141 (tt0) cc_final: 0.6683 (tt0) REVERT: F 31 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6582 (mp0) REVERT: F 42 LYS cc_start: 0.7304 (mtpp) cc_final: 0.6803 (mtmm) outliers start: 19 outliers final: 11 residues processed: 120 average time/residue: 1.1918 time to fit residues: 150.7186 Evaluate side-chains 120 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 74 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.0060 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN D 30 ASN E 16 GLN F 30 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7058 Z= 0.200 Angle : 0.530 6.287 9564 Z= 0.272 Chirality : 0.042 0.169 1054 Planarity : 0.005 0.050 1156 Dihedral : 10.703 130.512 1136 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.72 % Allowed : 14.17 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.80 (0.30), residues: 840 helix: 2.19 (0.27), residues: 304 sheet: 1.24 (0.34), residues: 240 loop : 0.16 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 110 HIS 0.003 0.001 HIS F 38 PHE 0.016 0.002 PHE A 39 TYR 0.012 0.001 TYR F 86 ARG 0.002 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.678 Fit side-chains REVERT: A 27 LYS cc_start: 0.6838 (ttmt) cc_final: 0.6351 (mttt) REVERT: A 134 LEU cc_start: 0.6725 (mt) cc_final: 0.6462 (mm) REVERT: A 138 LYS cc_start: 0.6678 (mptt) cc_final: 0.6384 (mptt) REVERT: A 139 GLU cc_start: 0.6677 (tt0) cc_final: 0.6410 (tt0) REVERT: B 27 LYS cc_start: 0.6946 (ttmt) cc_final: 0.6460 (mttt) REVERT: B 134 LEU cc_start: 0.6732 (mt) cc_final: 0.6472 (mm) REVERT: B 138 LYS cc_start: 0.6661 (mptt) cc_final: 0.6367 (mptt) REVERT: B 139 GLU cc_start: 0.6671 (tt0) cc_final: 0.6365 (tt0) REVERT: C 48 GLU cc_start: 0.7120 (tt0) cc_final: 0.6665 (tt0) REVERT: C 114 THR cc_start: 0.7345 (t) cc_final: 0.6990 (p) REVERT: D 31 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6609 (mp0) REVERT: D 42 LYS cc_start: 0.7271 (mtpp) cc_final: 0.6801 (mtmm) REVERT: D 61 ARG cc_start: 0.6788 (ptp90) cc_final: 0.6475 (ptp90) REVERT: E 48 GLU cc_start: 0.7179 (tt0) cc_final: 0.6730 (tt0) REVERT: F 31 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6628 (mp0) REVERT: F 42 LYS cc_start: 0.7313 (mtpp) cc_final: 0.6809 (mtmm) outliers start: 20 outliers final: 11 residues processed: 119 average time/residue: 1.3142 time to fit residues: 163.9879 Evaluate side-chains 125 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 112 GLN Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 74 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 0.0000 chunk 47 optimal weight: 0.8980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7058 Z= 0.148 Angle : 0.515 6.128 9564 Z= 0.263 Chirality : 0.040 0.169 1054 Planarity : 0.005 0.059 1156 Dihedral : 10.331 126.232 1136 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.04 % Allowed : 15.26 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.89 (0.30), residues: 840 helix: 2.33 (0.27), residues: 304 sheet: 1.26 (0.34), residues: 240 loop : 0.18 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 PHE 0.015 0.001 PHE B 39 TYR 0.010 0.001 TYR D 86 ARG 0.014 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 0.654 Fit side-chains REVERT: A 27 LYS cc_start: 0.6977 (ttmt) cc_final: 0.6477 (mttt) REVERT: A 29 ARG cc_start: 0.7065 (mtp180) cc_final: 0.6007 (mtm180) REVERT: A 134 LEU cc_start: 0.6699 (mt) cc_final: 0.6459 (mm) REVERT: A 138 LYS cc_start: 0.6594 (mptt) cc_final: 0.6329 (mptt) REVERT: A 139 GLU cc_start: 0.6703 (tt0) cc_final: 0.6406 (tt0) REVERT: B 27 LYS cc_start: 0.6963 (ttmt) cc_final: 0.6492 (mttt) REVERT: B 29 ARG cc_start: 0.7066 (mtp180) cc_final: 0.6008 (mtm180) REVERT: B 134 LEU cc_start: 0.6716 (mt) cc_final: 0.6477 (mm) REVERT: B 138 LYS cc_start: 0.6597 (mptt) cc_final: 0.6332 (mptt) REVERT: B 139 GLU cc_start: 0.6698 (tt0) cc_final: 0.6403 (tt0) REVERT: C 48 GLU cc_start: 0.7160 (tt0) cc_final: 0.6705 (tt0) REVERT: C 114 THR cc_start: 0.7358 (t) cc_final: 0.7028 (p) REVERT: D 31 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6655 (mp0) REVERT: D 42 LYS cc_start: 0.7235 (mtpp) cc_final: 0.6761 (mtmm) REVERT: D 61 ARG cc_start: 0.6852 (ptp90) cc_final: 0.6549 (ptp90) REVERT: E 48 GLU cc_start: 0.7152 (tt0) cc_final: 0.6704 (tt0) REVERT: F 31 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6587 (mp0) REVERT: F 42 LYS cc_start: 0.7283 (mtpp) cc_final: 0.6791 (mtmm) outliers start: 15 outliers final: 8 residues processed: 125 average time/residue: 1.2012 time to fit residues: 158.1384 Evaluate side-chains 125 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 39 optimal weight: 0.0670 chunk 51 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN F 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7058 Z= 0.161 Angle : 0.522 6.214 9564 Z= 0.266 Chirality : 0.041 0.170 1054 Planarity : 0.005 0.056 1156 Dihedral : 10.291 125.242 1136 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.23 % Allowed : 16.21 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.93 (0.30), residues: 840 helix: 2.29 (0.27), residues: 304 sheet: 1.34 (0.34), residues: 240 loop : 0.22 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 110 HIS 0.003 0.001 HIS E 52 PHE 0.016 0.001 PHE B 39 TYR 0.010 0.001 TYR F 86 ARG 0.013 0.001 ARG A 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.759 Fit side-chains REVERT: A 27 LYS cc_start: 0.6950 (ttmt) cc_final: 0.6492 (mttt) REVERT: A 29 ARG cc_start: 0.7081 (mtp180) cc_final: 0.6028 (mtm110) REVERT: A 134 LEU cc_start: 0.6693 (mt) cc_final: 0.6444 (mm) REVERT: A 138 LYS cc_start: 0.6602 (mptt) cc_final: 0.6328 (mptt) REVERT: A 139 GLU cc_start: 0.6755 (tt0) cc_final: 0.6462 (tt0) REVERT: B 27 LYS cc_start: 0.6950 (ttmt) cc_final: 0.6492 (mttt) REVERT: B 29 ARG cc_start: 0.7088 (mtp180) cc_final: 0.6036 (mtm110) REVERT: B 134 LEU cc_start: 0.6694 (mt) cc_final: 0.6450 (mm) REVERT: B 138 LYS cc_start: 0.6600 (mptt) cc_final: 0.6324 (mptt) REVERT: B 139 GLU cc_start: 0.6718 (tt0) cc_final: 0.6425 (tt0) REVERT: C 48 GLU cc_start: 0.7095 (tt0) cc_final: 0.6637 (tt0) REVERT: C 114 THR cc_start: 0.7298 (t) cc_final: 0.6973 (p) REVERT: D 31 GLU cc_start: 0.7399 (mt-10) cc_final: 0.6636 (mp0) REVERT: D 42 LYS cc_start: 0.7239 (mtpp) cc_final: 0.6766 (mtmm) REVERT: E 17 THR cc_start: 0.6357 (p) cc_final: 0.6003 (m) REVERT: E 48 GLU cc_start: 0.7079 (tt0) cc_final: 0.6631 (tt0) REVERT: F 31 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6597 (mp0) REVERT: F 42 LYS cc_start: 0.7273 (mtpp) cc_final: 0.6771 (mtmm) outliers start: 9 outliers final: 8 residues processed: 121 average time/residue: 1.0976 time to fit residues: 140.4971 Evaluate side-chains 121 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain F residue 74 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 30 ASN E 16 GLN F 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.160125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110676 restraints weight = 6871.587| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.11 r_work: 0.3056 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7058 Z= 0.189 Angle : 0.541 6.329 9564 Z= 0.274 Chirality : 0.041 0.174 1054 Planarity : 0.005 0.051 1156 Dihedral : 10.416 127.327 1136 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.36 % Allowed : 16.08 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.88 (0.30), residues: 840 helix: 2.20 (0.27), residues: 304 sheet: 1.33 (0.34), residues: 240 loop : 0.23 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 110 HIS 0.003 0.001 HIS F 38 PHE 0.017 0.002 PHE B 46 TYR 0.012 0.001 TYR F 86 ARG 0.013 0.001 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3177.26 seconds wall clock time: 56 minutes 18.40 seconds (3378.40 seconds total)