Starting phenix.real_space_refine on Tue Feb 13 11:57:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9a_10734/02_2024/6y9a_10734.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9a_10734/02_2024/6y9a_10734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9a_10734/02_2024/6y9a_10734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9a_10734/02_2024/6y9a_10734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9a_10734/02_2024/6y9a_10734.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9a_10734/02_2024/6y9a_10734.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.040 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: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 3829 2.51 5 N 965 2.21 5 O 1113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 102": "OD1" <-> "OD2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 150": "OD1" <-> "OD2" Residue "H TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 75": "OD1" <-> "OD2" Residue "L ASP 87": "OD1" <-> "OD2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 170": "OE1" <-> "OE2" Residue "L TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5948 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "B" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1310 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1644 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1684 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205} Time building chain proxies: 4.28, per 1000 atoms: 0.72 Number of scatterers: 5948 At special positions: 0 Unit cell: (61.864, 70.004, 154.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1113 8.00 N 965 7.00 C 3829 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 167 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 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: 2.46 Conformation dependent library (CDL) restraints added in 1.3 seconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 37.8% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 45 through 51 removed outlier: 5.150A pdb=" N LYS A 50 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 71 Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.617A pdb=" N THR A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 84' Processing helix chain 'A' and resid 85 through 103 removed outlier: 3.865A pdb=" N TRP A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 143 removed outlier: 3.917A pdb=" N LEU A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 171 through 176 removed outlier: 4.401A pdb=" N ASN A 176 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 210 Processing helix chain 'B' and resid 45 through 51 removed outlier: 5.825A pdb=" N LYS B 50 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 71 Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.646A pdb=" N VAL B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 100 removed outlier: 4.051A pdb=" N TRP B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 143 removed outlier: 3.710A pdb=" N LYS B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 171 through 176 removed outlier: 4.078A pdb=" N ASN B 176 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 212 removed outlier: 3.585A pdb=" N GLN B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'L' and resid 126 through 133 Processing helix chain 'L' and resid 188 through 193 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.723A pdb=" N LYS H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP H 59 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 19 through 21 removed outlier: 3.900A pdb=" N VAL H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET H 81 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR H 80 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR H 69 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.563A pdb=" N LEU H 130 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA H 143 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 190 " --> pdb=" O ALA H 143 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N GLY H 145 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL H 188 " --> pdb=" O GLY H 145 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU H 147 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N SER H 186 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS H 149 " --> pdb=" O LEU H 184 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU H 184 " --> pdb=" O LYS H 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.635A pdb=" N THR H 157 " --> pdb=" O ASN H 205 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL H 204 " --> pdb=" O VAL H 213 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL H 213 " --> pdb=" O VAL H 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.739A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER L 22 " --> pdb=" O THR L 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.572A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR L 39 " --> pdb=" O ALA L 94 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.572A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN L 95 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 68 through 71 Processing sheet with id=AB1, first strand: chain 'L' and resid 120 through 123 removed outlier: 3.646A pdb=" N PHE L 123 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU L 184 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS L 139 " --> pdb=" O SER L 182 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER L 182 " --> pdb=" O CYS L 139 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU L 141 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 158 through 159 removed outlier: 3.972A pdb=" N LYS L 150 " --> pdb=" O THR L 202 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR L 202 " --> pdb=" O LYS L 150 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN L 152 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU L 200 " --> pdb=" O GLN L 152 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS L 154 " --> pdb=" O ALA L 198 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR L 197 " --> pdb=" O PHE L 214 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE L 214 " --> pdb=" O TYR L 197 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS L 212 " --> pdb=" O CYS L 199 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL L 210 " --> pdb=" O VAL L 201 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 717 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: 2.04 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1839 1.34 - 1.46: 1465 1.46 - 1.58: 2714 1.58 - 1.70: 2 1.70 - 1.82: 65 Bond restraints: 6085 Sorted by residual: bond pdb=" CB PRO A 79 " pdb=" CG PRO A 79 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.61e+00 bond pdb=" CB PRO A 73 " pdb=" CG PRO A 73 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.70e+00 bond pdb=" CG1 ILE A 141 " pdb=" CD1 ILE A 141 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.50e+00 bond pdb=" CA THR B 180 " pdb=" C THR B 180 " ideal model delta sigma weight residual 1.520 1.504 0.015 1.40e-02 5.10e+03 1.21e+00 bond pdb=" N PRO B 73 " pdb=" CA PRO B 73 " ideal model delta sigma weight residual 1.469 1.482 -0.013 1.28e-02 6.10e+03 1.10e+00 ... (remaining 6080 not shown) Histogram of bond angle deviations from ideal: 96.37 - 103.90: 106 103.90 - 111.43: 2570 111.43 - 118.97: 2331 118.97 - 126.50: 3160 126.50 - 134.03: 90 Bond angle restraints: 8257 Sorted by residual: angle pdb=" CA PRO A 79 " pdb=" N PRO A 79 " pdb=" CD PRO A 79 " ideal model delta sigma weight residual 112.00 105.14 6.86 1.40e+00 5.10e-01 2.40e+01 angle pdb=" CA PRO A 73 " pdb=" N PRO A 73 " pdb=" CD PRO A 73 " ideal model delta sigma weight residual 112.00 105.64 6.36 1.40e+00 5.10e-01 2.06e+01 angle pdb=" N LYS B 148 " pdb=" CA LYS B 148 " pdb=" C LYS B 148 " ideal model delta sigma weight residual 111.03 115.64 -4.61 1.11e+00 8.12e-01 1.73e+01 angle pdb=" N GLN A 181 " pdb=" CA GLN A 181 " pdb=" C GLN A 181 " ideal model delta sigma weight residual 111.28 106.77 4.51 1.09e+00 8.42e-01 1.71e+01 angle pdb=" N GLN B 181 " pdb=" CA GLN B 181 " pdb=" C GLN B 181 " ideal model delta sigma weight residual 111.28 107.01 4.27 1.09e+00 8.42e-01 1.54e+01 ... (remaining 8252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 3284 17.24 - 34.48: 278 34.48 - 51.72: 61 51.72 - 68.96: 10 68.96 - 86.20: 7 Dihedral angle restraints: 3640 sinusoidal: 1404 harmonic: 2236 Sorted by residual: dihedral pdb=" CB CYS L 139 " pdb=" SG CYS L 139 " pdb=" SG CYS L 199 " pdb=" CB CYS L 199 " ideal model delta sinusoidal sigma weight residual 93.00 176.92 -83.92 1 1.00e+01 1.00e-02 8.58e+01 dihedral pdb=" CB CYS H 146 " pdb=" SG CYS H 146 " pdb=" SG CYS H 202 " pdb=" CB CYS H 202 " ideal model delta sinusoidal sigma weight residual 93.00 16.07 76.93 1 1.00e+01 1.00e-02 7.43e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 18.32 74.68 1 1.00e+01 1.00e-02 7.06e+01 ... (remaining 3637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 750 0.058 - 0.116: 171 0.116 - 0.175: 20 0.175 - 0.233: 3 0.233 - 0.291: 1 Chirality restraints: 945 Sorted by residual: chirality pdb=" CG LEU B 122 " pdb=" CB LEU B 122 " pdb=" CD1 LEU B 122 " pdb=" CD2 LEU B 122 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB VAL H 190 " pdb=" CA VAL H 190 " pdb=" CG1 VAL H 190 " pdb=" CG2 VAL H 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLN L 55 " pdb=" N GLN L 55 " pdb=" C GLN L 55 " pdb=" CB GLN L 55 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 942 not shown) Planarity restraints: 1030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 179 " 0.031 2.00e-02 2.50e+03 6.11e-02 3.73e+01 pdb=" C SER B 179 " -0.106 2.00e-02 2.50e+03 pdb=" O SER B 179 " 0.038 2.00e-02 2.50e+03 pdb=" N THR B 180 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 179 " -0.028 2.00e-02 2.50e+03 5.47e-02 3.00e+01 pdb=" C SER A 179 " 0.095 2.00e-02 2.50e+03 pdb=" O SER A 179 " -0.035 2.00e-02 2.50e+03 pdb=" N THR A 180 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 116 " -0.026 2.00e-02 2.50e+03 5.19e-02 2.69e+01 pdb=" C LYS B 116 " 0.090 2.00e-02 2.50e+03 pdb=" O LYS B 116 " -0.034 2.00e-02 2.50e+03 pdb=" N MET B 117 " -0.030 2.00e-02 2.50e+03 ... (remaining 1027 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 566 2.75 - 3.29: 6136 3.29 - 3.82: 9405 3.82 - 4.36: 10399 4.36 - 4.90: 17289 Nonbonded interactions: 43795 Sorted by model distance: nonbonded pdb=" O GLY H 103 " pdb=" OH TYR L 39 " model vdw 2.211 2.440 nonbonded pdb=" O TYR L 191 " pdb=" OH TYR L 197 " model vdw 2.271 2.440 nonbonded pdb=" O HIS L 194 " pdb=" NH2 ARG L 216 " model vdw 2.281 2.520 nonbonded pdb=" OG1 THR H 199 " pdb=" OE2 GLU H 218 " model vdw 2.312 2.440 nonbonded pdb=" ND2 ASN A 163 " pdb=" OD1 ASN A 166 " model vdw 2.328 2.520 ... (remaining 43790 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' } 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 group one per residue 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: 4.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.990 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.340 Find NCS groups from input model: 0.220 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4803 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 0.107 6085 Z= 0.226 Angle : 0.809 10.221 8257 Z= 0.443 Chirality : 0.050 0.291 945 Planarity : 0.008 0.127 1030 Dihedral : 13.593 86.201 2192 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: -1.17 (0.29), residues: 766 helix: -0.51 (0.30), residues: 228 sheet: 0.10 (0.38), residues: 174 loop : -1.35 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 109 HIS 0.005 0.001 HIS B 63 PHE 0.040 0.002 PHE B 62 TYR 0.014 0.001 TYR L 197 ARG 0.005 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 MET cc_start: 0.4432 (mmm) cc_final: 0.4113 (mmm) REVERT: A 117 MET cc_start: 0.8031 (ptt) cc_final: 0.6042 (tpt) REVERT: B 149 MET cc_start: 0.7266 (mpp) cc_final: 0.6631 (mpp) REVERT: L 42 LEU cc_start: 0.6631 (tt) cc_final: 0.6234 (tt) REVERT: L 56 MET cc_start: 0.7262 (tmm) cc_final: 0.7059 (tmm) REVERT: L 146 PRO cc_start: 0.6978 (Cg_endo) cc_final: 0.6457 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1575 time to fit residues: 40.5953 Evaluate side-chains 155 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 0.0270 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN A 204 GLN B 120 ASN H 39 GLN H 161 ASN ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN L 129 GLN L 194 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5022 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6085 Z= 0.168 Angle : 0.602 6.397 8257 Z= 0.313 Chirality : 0.043 0.166 945 Planarity : 0.006 0.069 1030 Dihedral : 4.530 15.667 824 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.15 % Allowed : 5.85 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: -0.04 (0.30), residues: 766 helix: 0.96 (0.32), residues: 245 sheet: 0.74 (0.38), residues: 177 loop : -1.17 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 33 HIS 0.004 0.001 HIS A 63 PHE 0.023 0.002 PHE B 62 TYR 0.017 0.001 TYR L 54 ARG 0.009 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8235 (ptt) cc_final: 0.6271 (tpt) REVERT: B 100 LEU cc_start: 0.8034 (mp) cc_final: 0.7828 (mm) REVERT: B 149 MET cc_start: 0.6990 (mpp) cc_final: 0.6662 (mpp) REVERT: H 100 VAL cc_start: 0.7415 (t) cc_final: 0.6856 (t) REVERT: L 42 LEU cc_start: 0.6365 (tt) cc_final: 0.5994 (tt) REVERT: L 56 MET cc_start: 0.7648 (tmm) cc_final: 0.7071 (tmm) REVERT: L 80 ILE cc_start: 0.3552 (mp) cc_final: 0.3073 (mm) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.1503 time to fit residues: 38.3709 Evaluate side-chains 154 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 18 optimal weight: 0.5980 chunk 67 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 66 optimal weight: 0.0980 chunk 22 optimal weight: 0.0040 chunk 54 optimal weight: 8.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 ASN ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5001 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6085 Z= 0.143 Angle : 0.575 8.055 8257 Z= 0.295 Chirality : 0.043 0.174 945 Planarity : 0.005 0.059 1030 Dihedral : 4.245 15.083 824 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.15 % Allowed : 3.30 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: 0.32 (0.30), residues: 766 helix: 1.57 (0.33), residues: 237 sheet: 0.77 (0.39), residues: 171 loop : -1.01 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 33 HIS 0.003 0.001 HIS A 63 PHE 0.026 0.001 PHE B 62 TYR 0.015 0.001 TYR L 54 ARG 0.006 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8372 (ptt) cc_final: 0.8121 (ptt) REVERT: B 149 MET cc_start: 0.6933 (mpp) cc_final: 0.6712 (mpp) REVERT: L 56 MET cc_start: 0.7722 (tmm) cc_final: 0.7194 (tmm) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.1327 time to fit residues: 32.9998 Evaluate side-chains 151 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 HIS ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN L 143 ASN ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5631 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6085 Z= 0.290 Angle : 0.712 7.876 8257 Z= 0.372 Chirality : 0.045 0.159 945 Planarity : 0.006 0.054 1030 Dihedral : 5.072 18.344 824 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: -0.03 (0.31), residues: 766 helix: 0.88 (0.32), residues: 258 sheet: 0.16 (0.37), residues: 186 loop : -0.80 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 89 HIS 0.006 0.001 HIS L 31 PHE 0.024 0.003 PHE L 76 TYR 0.022 0.002 TYR L 54 ARG 0.009 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8643 (ptt) cc_final: 0.8336 (ptt) REVERT: B 149 MET cc_start: 0.6999 (mpp) cc_final: 0.6429 (mpp) REVERT: B 150 GLU cc_start: 0.6854 (pp20) cc_final: 0.6565 (pp20) REVERT: B 184 TYR cc_start: 0.7013 (m-10) cc_final: 0.6806 (m-10) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1420 time to fit residues: 33.5696 Evaluate side-chains 147 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6085 Z= 0.209 Angle : 0.624 7.242 8257 Z= 0.324 Chirality : 0.043 0.183 945 Planarity : 0.005 0.057 1030 Dihedral : 4.665 17.282 824 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: 0.05 (0.31), residues: 766 helix: 1.05 (0.33), residues: 260 sheet: 0.16 (0.36), residues: 181 loop : -0.81 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP H 36 HIS 0.005 0.001 HIS A 63 PHE 0.023 0.002 PHE B 62 TYR 0.019 0.002 TYR L 54 ARG 0.004 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8717 (ptt) cc_final: 0.8413 (ptp) REVERT: A 131 MET cc_start: 0.7328 (mmm) cc_final: 0.6919 (ttt) REVERT: B 150 GLU cc_start: 0.7011 (pp20) cc_final: 0.6690 (pp20) REVERT: B 175 LYS cc_start: 0.6300 (mmmt) cc_final: 0.6094 (tppt) REVERT: B 184 TYR cc_start: 0.7005 (m-10) cc_final: 0.6757 (m-10) REVERT: L 146 PRO cc_start: 0.7189 (Cg_exo) cc_final: 0.6841 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1342 time to fit residues: 33.8823 Evaluate side-chains 147 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5507 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6085 Z= 0.170 Angle : 0.614 8.410 8257 Z= 0.312 Chirality : 0.043 0.162 945 Planarity : 0.005 0.056 1030 Dihedral : 4.510 16.806 824 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: 0.21 (0.31), residues: 766 helix: 1.18 (0.33), residues: 260 sheet: 0.28 (0.36), residues: 183 loop : -0.75 (0.37), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 40 HIS 0.004 0.001 HIS A 63 PHE 0.020 0.002 PHE B 62 TYR 0.013 0.001 TYR L 54 ARG 0.005 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8820 (ptt) cc_final: 0.8454 (ptm) REVERT: A 131 MET cc_start: 0.7311 (mmm) cc_final: 0.7067 (ttt) REVERT: B 119 MET cc_start: 0.7473 (tpt) cc_final: 0.7180 (mmm) REVERT: B 131 MET cc_start: 0.6907 (mmm) cc_final: 0.6662 (mmm) REVERT: B 149 MET cc_start: 0.6675 (mpp) cc_final: 0.6108 (mpp) REVERT: L 56 MET cc_start: 0.7394 (tmm) cc_final: 0.6535 (tmm) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1385 time to fit residues: 34.7773 Evaluate side-chains 149 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 52 optimal weight: 0.0170 chunk 60 optimal weight: 0.0020 chunk 39 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 43 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN L 58 ASN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6085 Z= 0.186 Angle : 0.631 8.067 8257 Z= 0.323 Chirality : 0.044 0.167 945 Planarity : 0.005 0.054 1030 Dihedral : 4.511 17.179 824 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: 0.17 (0.31), residues: 766 helix: 1.21 (0.33), residues: 258 sheet: 0.00 (0.36), residues: 191 loop : -0.65 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP L 40 HIS 0.003 0.001 HIS B 158 PHE 0.025 0.002 PHE A 190 TYR 0.013 0.001 TYR L 54 ARG 0.004 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8831 (ptt) cc_final: 0.8481 (ptm) REVERT: B 92 ILE cc_start: 0.8322 (tp) cc_final: 0.8101 (tp) REVERT: B 119 MET cc_start: 0.7369 (tpt) cc_final: 0.7003 (mmm) REVERT: B 131 MET cc_start: 0.6823 (mmm) cc_final: 0.6519 (mmm) REVERT: B 149 MET cc_start: 0.6631 (mpp) cc_final: 0.6037 (mpp) REVERT: B 150 GLU cc_start: 0.7120 (pp20) cc_final: 0.6863 (pp20) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1306 time to fit residues: 33.1944 Evaluate side-chains 151 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.0000 chunk 21 optimal weight: 0.0470 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 45 optimal weight: 0.0270 chunk 48 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 64 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5392 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6085 Z= 0.152 Angle : 0.628 10.409 8257 Z= 0.313 Chirality : 0.043 0.172 945 Planarity : 0.005 0.053 1030 Dihedral : 4.378 15.978 824 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: 0.29 (0.31), residues: 766 helix: 1.20 (0.33), residues: 258 sheet: 0.42 (0.37), residues: 182 loop : -0.71 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 33 HIS 0.003 0.001 HIS L 31 PHE 0.026 0.002 PHE B 62 TYR 0.014 0.001 TYR B 184 ARG 0.005 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8843 (ptt) cc_final: 0.8460 (ptm) REVERT: B 119 MET cc_start: 0.7209 (tpt) cc_final: 0.6826 (mmm) REVERT: B 150 GLU cc_start: 0.7116 (pp20) cc_final: 0.6857 (pp20) REVERT: L 146 PRO cc_start: 0.7052 (Cg_endo) cc_final: 0.6740 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1433 time to fit residues: 33.8983 Evaluate side-chains 146 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 0.0470 chunk 20 optimal weight: 0.1980 chunk 60 optimal weight: 0.0970 chunk 43 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 0.1980 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN L 58 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5356 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6085 Z= 0.156 Angle : 0.639 8.701 8257 Z= 0.319 Chirality : 0.044 0.168 945 Planarity : 0.005 0.052 1030 Dihedral : 4.339 18.837 824 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: 0.34 (0.31), residues: 766 helix: 1.23 (0.33), residues: 258 sheet: 0.50 (0.38), residues: 183 loop : -0.71 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 36 HIS 0.003 0.001 HIS L 31 PHE 0.028 0.001 PHE B 62 TYR 0.035 0.001 TYR L 54 ARG 0.003 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8853 (ptt) cc_final: 0.8466 (ptm) REVERT: B 119 MET cc_start: 0.7115 (tpt) cc_final: 0.6884 (mmm) REVERT: B 131 MET cc_start: 0.6350 (mmm) cc_final: 0.6108 (mmm) REVERT: B 149 MET cc_start: 0.6559 (mpp) cc_final: 0.6354 (mpp) REVERT: B 150 GLU cc_start: 0.7061 (pp20) cc_final: 0.6860 (pp20) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1403 time to fit residues: 33.8242 Evaluate side-chains 144 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 5.9990 chunk 48 optimal weight: 0.1980 chunk 73 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 45 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN L 58 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5547 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6085 Z= 0.194 Angle : 0.629 7.413 8257 Z= 0.323 Chirality : 0.044 0.207 945 Planarity : 0.005 0.062 1030 Dihedral : 4.456 15.465 824 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: 0.26 (0.31), residues: 766 helix: 1.16 (0.33), residues: 258 sheet: 0.19 (0.36), residues: 195 loop : -0.59 (0.38), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 40 HIS 0.005 0.001 HIS L 31 PHE 0.024 0.002 PHE B 62 TYR 0.021 0.001 TYR L 54 ARG 0.004 0.001 ARG L 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 MET cc_start: 0.8884 (ptt) cc_final: 0.8507 (ptm) REVERT: B 119 MET cc_start: 0.7320 (tpt) cc_final: 0.7024 (mmm) REVERT: B 131 MET cc_start: 0.6537 (mmm) cc_final: 0.6241 (mmm) REVERT: B 149 MET cc_start: 0.6651 (mpp) cc_final: 0.6356 (mpp) REVERT: B 150 GLU cc_start: 0.7185 (pp20) cc_final: 0.6934 (pp20) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1379 time to fit residues: 33.9908 Evaluate side-chains 140 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 30.0000 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 51 optimal weight: 0.0370 chunk 3 optimal weight: 5.9990 chunk 42 optimal weight: 0.1980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN L 55 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.135834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.104315 restraints weight = 14638.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.109435 restraints weight = 9330.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.113438 restraints weight = 6580.817| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6085 Z= 0.164 Angle : 0.619 7.439 8257 Z= 0.314 Chirality : 0.043 0.212 945 Planarity : 0.005 0.053 1030 Dihedral : 4.329 15.080 824 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % 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: 0.30 (0.31), residues: 766 helix: 1.26 (0.33), residues: 260 sheet: 0.09 (0.36), residues: 197 loop : -0.55 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 36 HIS 0.003 0.001 HIS L 31 PHE 0.028 0.002 PHE B 62 TYR 0.014 0.001 TYR L 54 ARG 0.004 0.000 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1733.02 seconds wall clock time: 32 minutes 24.15 seconds (1944.15 seconds total)