Starting phenix.real_space_refine on Wed Sep 17 06:12:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6y9a_10734/09_2025/6y9a_10734.cif Found real_map, /net/cci-nas-00/data/ceres_data/6y9a_10734/09_2025/6y9a_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/cci-nas-00/data/ceres_data/6y9a_10734/09_2025/6y9a_10734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6y9a_10734/09_2025/6y9a_10734.map" model { file = "/net/cci-nas-00/data/ceres_data/6y9a_10734/09_2025/6y9a_10734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6y9a_10734/09_2025/6y9a_10734.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.63, per 1000 atoms: 0.27 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 232.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.20 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: 0.93 Time building geometry restraints manager: 0.64 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: 0.00 - 2.04: 7992 2.04 - 4.09: 221 4.09 - 6.13: 35 6.13 - 8.18: 7 8.18 - 10.22: 2 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 3.040 nonbonded pdb=" O TYR L 191 " pdb=" OH TYR L 197 " model vdw 2.271 3.040 nonbonded pdb=" O HIS L 194 " pdb=" NH2 ARG L 216 " model vdw 2.281 3.120 nonbonded pdb=" OG1 THR H 199 " pdb=" OE2 GLU H 218 " model vdw 2.312 3.040 nonbonded pdb=" ND2 ASN A 163 " pdb=" OD1 ASN A 166 " model vdw 2.328 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 4.190 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.240 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.170 ------------------------------------------------------------------------------- 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 6091 Z= 0.153 Angle : 0.809 10.221 8269 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG H 98 TYR 0.014 0.001 TYR L 197 PHE 0.040 0.002 PHE B 62 TRP 0.026 0.001 TRP H 109 HIS 0.005 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6085) covalent geometry : angle 0.80880 ( 8257) SS BOND : bond 0.00433 ( 6) SS BOND : angle 1.14637 ( 12) hydrogen bonds : bond 0.19682 ( 263) hydrogen bonds : angle 6.69154 ( 717) *********************** 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 to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.224 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: 0.4112 (mmm) REVERT: A 117 MET cc_start: 0.8031 (ptt) cc_final: 0.6041 (tpt) REVERT: B 149 MET cc_start: 0.7266 (mpp) cc_final: 0.6624 (mpp) REVERT: L 42 LEU cc_start: 0.6631 (tt) cc_final: 0.6238 (tt) REVERT: L 56 MET cc_start: 0.7262 (tmm) cc_final: 0.6827 (ppp) REVERT: L 146 PRO cc_start: 0.6978 (Cg_endo) cc_final: 0.6463 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0661 time to fit residues: 17.4143 Evaluate side-chains 155 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.0670 chunk 61 optimal weight: 0.0020 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.3126 ------------------------------------------------------------------------------- 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 L 47 GLN L 194 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.158640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.125153 restraints weight = 15276.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.130523 restraints weight = 10311.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.134712 restraints weight = 7449.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.138129 restraints weight = 5675.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.140755 restraints weight = 4476.505| |-----------------------------------------------------------------------------| r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6091 Z= 0.118 Angle : 0.614 6.730 8269 Z= 0.319 Chirality : 0.044 0.166 945 Planarity : 0.006 0.068 1030 Dihedral : 4.565 19.524 824 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.15 % Allowed : 4.50 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.30), residues: 766 helix: 0.87 (0.33), residues: 241 sheet: 0.74 (0.42), residues: 157 loop : -1.17 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 98 TYR 0.017 0.001 TYR L 54 PHE 0.025 0.001 PHE B 62 TRP 0.025 0.002 TRP H 33 HIS 0.003 0.001 HIS A 63 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 6085) covalent geometry : angle 0.61365 ( 8257) SS BOND : bond 0.00346 ( 6) SS BOND : angle 0.84777 ( 12) hydrogen bonds : bond 0.03654 ( 263) hydrogen bonds : angle 4.69859 ( 717) *********************** 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 195 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 0.240 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: 0.7775 (ptt) cc_final: 0.6438 (tpt) REVERT: A 119 MET cc_start: 0.8915 (mmp) cc_final: 0.8666 (mmm) REVERT: A 164 ILE cc_start: 0.8035 (mt) cc_final: 0.7760 (mp) REVERT: A 176 ASN cc_start: 0.8068 (m-40) cc_final: 0.7614 (m-40) REVERT: A 190 PHE cc_start: 0.8821 (m-10) cc_final: 0.8469 (m-80) REVERT: B 58 MET cc_start: 0.8730 (ttm) cc_final: 0.8366 (ttt) REVERT: B 62 PHE cc_start: 0.8578 (m-80) cc_final: 0.8150 (m-80) REVERT: B 119 MET cc_start: 0.8513 (tpt) cc_final: 0.8282 (tpt) REVERT: B 131 MET cc_start: 0.7501 (mmp) cc_final: 0.7191 (mmm) REVERT: B 149 MET cc_start: 0.7420 (mpp) cc_final: 0.6744 (mpp) REVERT: B 150 GLU cc_start: 0.7778 (pp20) cc_final: 0.7447 (pp20) REVERT: B 184 TYR cc_start: 0.8228 (m-10) cc_final: 0.7774 (m-10) REVERT: B 211 ILE cc_start: 0.7332 (mm) cc_final: 0.7129 (mm) REVERT: H 22 CYS cc_start: 0.4924 (p) cc_final: 0.4506 (p) REVERT: H 35 ASN cc_start: 0.8647 (p0) cc_final: 0.8367 (p0) REVERT: H 36 TRP cc_start: 0.7933 (m100) cc_final: 0.7434 (m100) REVERT: H 73 ASP cc_start: 0.9290 (t0) cc_final: 0.9000 (t0) REVERT: H 99 ASN cc_start: 0.8136 (t0) cc_final: 0.7547 (p0) REVERT: H 100 VAL cc_start: 0.8851 (t) cc_final: 0.8263 (t) REVERT: H 128 PHE cc_start: 0.8814 (m-80) cc_final: 0.8601 (m-80) REVERT: H 201 ILE cc_start: 0.8348 (tp) cc_final: 0.8068 (tp) REVERT: L 79 LYS cc_start: 0.7831 (tptt) cc_final: 0.7201 (tppt) REVERT: L 80 ILE cc_start: 0.7033 (mp) cc_final: 0.6620 (mm) REVERT: L 91 TYR cc_start: 0.9073 (m-10) cc_final: 0.8366 (m-80) REVERT: L 123 PHE cc_start: 0.7965 (m-80) cc_final: 0.7573 (m-80) REVERT: L 175 ASP cc_start: 0.8683 (m-30) cc_final: 0.8454 (m-30) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.0594 time to fit residues: 16.1671 Evaluate side-chains 163 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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** B 120 ASN B 158 HIS L 47 GLN L 129 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.155121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.120421 restraints weight = 14168.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.125673 restraints weight = 9561.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.129905 restraints weight = 6931.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.133343 restraints weight = 5288.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.136008 restraints weight = 4173.139| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6091 Z= 0.107 Angle : 0.574 7.209 8269 Z= 0.296 Chirality : 0.043 0.171 945 Planarity : 0.005 0.058 1030 Dihedral : 4.294 17.507 824 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.15 % Allowed : 3.15 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.30), residues: 766 helix: 1.44 (0.33), residues: 233 sheet: 0.82 (0.39), residues: 175 loop : -1.04 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.016 0.001 TYR L 54 PHE 0.018 0.001 PHE B 62 TRP 0.022 0.002 TRP H 33 HIS 0.007 0.001 HIS B 158 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 6085) covalent geometry : angle 0.57359 ( 8257) SS BOND : bond 0.00378 ( 6) SS BOND : angle 0.98866 ( 12) hydrogen bonds : bond 0.03453 ( 263) hydrogen bonds : angle 4.34220 ( 717) *********************** 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 186 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8913 (mmp) cc_final: 0.8686 (mmm) REVERT: A 164 ILE cc_start: 0.8096 (mt) cc_final: 0.7775 (mp) REVERT: A 181 GLN cc_start: 0.8948 (mt0) cc_final: 0.8628 (tp40) REVERT: A 190 PHE cc_start: 0.8913 (m-10) cc_final: 0.8499 (m-80) REVERT: B 58 MET cc_start: 0.8660 (ttm) cc_final: 0.8360 (ttt) REVERT: B 62 PHE cc_start: 0.8619 (m-80) cc_final: 0.8181 (m-80) REVERT: B 119 MET cc_start: 0.8513 (tpt) cc_final: 0.8175 (tpt) REVERT: B 140 ASN cc_start: 0.7325 (m110) cc_final: 0.7097 (m110) REVERT: B 149 MET cc_start: 0.7131 (mpp) cc_final: 0.6501 (mpp) REVERT: B 150 GLU cc_start: 0.7579 (pp20) cc_final: 0.7177 (pp20) REVERT: B 161 TYR cc_start: 0.6715 (m-80) cc_final: 0.6327 (m-80) REVERT: B 174 GLU cc_start: 0.9166 (mp0) cc_final: 0.8854 (mp0) REVERT: B 184 TYR cc_start: 0.8290 (m-10) cc_final: 0.7870 (m-10) REVERT: B 211 ILE cc_start: 0.7356 (mm) cc_final: 0.7125 (mm) REVERT: H 22 CYS cc_start: 0.5356 (p) cc_final: 0.4789 (p) REVERT: H 36 TRP cc_start: 0.8270 (m100) cc_final: 0.7661 (m100) REVERT: H 47 TRP cc_start: 0.7090 (t60) cc_final: 0.6764 (t60) REVERT: H 73 ASP cc_start: 0.9291 (t0) cc_final: 0.9017 (t0) REVERT: H 104 TYR cc_start: 0.7363 (m-10) cc_final: 0.7145 (m-10) REVERT: H 201 ILE cc_start: 0.8408 (tp) cc_final: 0.8132 (tp) REVERT: L 76 PHE cc_start: 0.7560 (m-80) cc_final: 0.7014 (m-80) REVERT: L 91 TYR cc_start: 0.9195 (m-10) cc_final: 0.8635 (m-80) REVERT: L 123 PHE cc_start: 0.8257 (m-80) cc_final: 0.7854 (m-80) REVERT: L 175 ASP cc_start: 0.8657 (m-30) cc_final: 0.8410 (m-30) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.0559 time to fit residues: 14.7085 Evaluate side-chains 154 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 70 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 56 optimal weight: 0.0770 chunk 61 optimal weight: 0.2980 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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** B 56 GLN B 120 ASN L 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.153771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.118892 restraints weight = 14205.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.124164 restraints weight = 9630.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.128244 restraints weight = 7012.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.131684 restraints weight = 5347.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.134287 restraints weight = 4234.971| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6091 Z= 0.102 Angle : 0.563 7.271 8269 Z= 0.288 Chirality : 0.042 0.169 945 Planarity : 0.005 0.056 1030 Dihedral : 4.177 16.954 824 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.30), residues: 766 helix: 1.86 (0.33), residues: 237 sheet: 0.89 (0.38), residues: 181 loop : -0.90 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.014 0.001 TYR L 54 PHE 0.015 0.001 PHE B 62 TRP 0.016 0.001 TRP H 33 HIS 0.002 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 6085) covalent geometry : angle 0.56241 ( 8257) SS BOND : bond 0.00406 ( 6) SS BOND : angle 0.94520 ( 12) hydrogen bonds : bond 0.03346 ( 263) hydrogen bonds : angle 4.08532 ( 717) *********************** 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 183 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8958 (mmp) cc_final: 0.8724 (mmm) REVERT: A 164 ILE cc_start: 0.8137 (mt) cc_final: 0.7900 (mp) REVERT: A 176 ASN cc_start: 0.8340 (m-40) cc_final: 0.7996 (m-40) REVERT: A 181 GLN cc_start: 0.8974 (mt0) cc_final: 0.8653 (tp40) REVERT: A 190 PHE cc_start: 0.8963 (m-10) cc_final: 0.8679 (m-80) REVERT: B 58 MET cc_start: 0.8680 (ttm) cc_final: 0.8298 (ttt) REVERT: B 62 PHE cc_start: 0.8595 (m-80) cc_final: 0.8155 (m-80) REVERT: B 119 MET cc_start: 0.8327 (tpt) cc_final: 0.8113 (tpt) REVERT: B 131 MET cc_start: 0.7308 (mmm) cc_final: 0.7072 (mmm) REVERT: B 140 ASN cc_start: 0.7401 (m110) cc_final: 0.7094 (m110) REVERT: B 149 MET cc_start: 0.7140 (mpp) cc_final: 0.6549 (mpp) REVERT: B 150 GLU cc_start: 0.7469 (pp20) cc_final: 0.7044 (pp20) REVERT: B 161 TYR cc_start: 0.6751 (m-80) cc_final: 0.6345 (m-80) REVERT: B 176 ASN cc_start: 0.7837 (m-40) cc_final: 0.7198 (p0) REVERT: B 184 TYR cc_start: 0.8363 (m-10) cc_final: 0.7906 (m-10) REVERT: B 211 ILE cc_start: 0.7427 (mm) cc_final: 0.7184 (mm) REVERT: H 73 ASP cc_start: 0.9340 (t0) cc_final: 0.9061 (t0) REVERT: H 201 ILE cc_start: 0.8430 (tp) cc_final: 0.8151 (tp) REVERT: L 21 ILE cc_start: 0.7542 (tp) cc_final: 0.7268 (tp) REVERT: L 76 PHE cc_start: 0.7327 (m-80) cc_final: 0.7099 (m-80) REVERT: L 91 TYR cc_start: 0.9095 (m-10) cc_final: 0.8547 (m-80) REVERT: L 123 PHE cc_start: 0.8341 (m-80) cc_final: 0.7897 (m-80) REVERT: L 175 ASP cc_start: 0.8656 (m-30) cc_final: 0.8417 (m-30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.0553 time to fit residues: 14.3759 Evaluate side-chains 156 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.7648 > 50: distance: 62 - 190: 28.028 distance: 95 - 191: 22.635 distance: 114 - 176: 7.611 distance: 117 - 173: 21.278 distance: 130 - 157: 12.440 distance: 133 - 154: 9.721 distance: 152 - 154: 6.493 distance: 154 - 155: 11.318 distance: 155 - 156: 15.209 distance: 155 - 158: 7.042 distance: 156 - 157: 15.689 distance: 156 - 161: 36.759 distance: 158 - 159: 11.825 distance: 158 - 160: 18.981 distance: 161 - 162: 30.757 distance: 161 - 282: 25.798 distance: 162 - 163: 47.490 distance: 162 - 165: 13.609 distance: 163 - 164: 32.621 distance: 163 - 173: 50.805 distance: 164 - 279: 15.844 distance: 165 - 166: 7.202 distance: 166 - 167: 13.908 distance: 167 - 169: 6.516 distance: 168 - 170: 8.784 distance: 169 - 171: 4.135 distance: 170 - 171: 9.983 distance: 171 - 172: 8.219 distance: 173 - 174: 31.662 distance: 174 - 175: 7.301 distance: 174 - 177: 10.770 distance: 175 - 176: 24.352 distance: 175 - 185: 33.137 distance: 177 - 178: 7.098 distance: 178 - 179: 7.122 distance: 178 - 180: 10.549 distance: 179 - 181: 10.369 distance: 180 - 182: 15.099 distance: 181 - 183: 11.668 distance: 182 - 183: 10.993 distance: 183 - 184: 7.529 distance: 185 - 186: 15.790 distance: 186 - 187: 24.153 distance: 186 - 189: 25.461 distance: 187 - 188: 3.888 distance: 187 - 191: 22.566 distance: 189 - 190: 29.986 distance: 191 - 192: 6.631 distance: 192 - 193: 20.102 distance: 192 - 195: 14.015 distance: 193 - 194: 12.097 distance: 193 - 196: 11.964 distance: 196 - 197: 13.350 distance: 197 - 198: 10.881 distance: 197 - 200: 7.318 distance: 198 - 199: 11.854 distance: 198 - 205: 9.662 distance: 200 - 201: 4.177 distance: 201 - 202: 4.729 distance: 202 - 203: 5.405 distance: 202 - 204: 5.986 distance: 205 - 206: 6.463 distance: 206 - 207: 3.179 distance: 207 - 208: 24.270 distance: 207 - 213: 22.028 distance: 209 - 210: 5.427 distance: 210 - 211: 5.555 distance: 210 - 212: 5.769 distance: 213 - 214: 3.074 distance: 214 - 215: 12.196 distance: 214 - 217: 12.077 distance: 215 - 216: 31.161 distance: 215 - 221: 18.265 distance: 217 - 218: 18.083 distance: 218 - 219: 12.305 distance: 218 - 220: 13.008 distance: 221 - 222: 18.500 distance: 222 - 223: 14.746 distance: 222 - 225: 27.873 distance: 223 - 224: 24.661 distance: 223 - 230: 15.041 distance: 225 - 226: 12.368 distance: 226 - 227: 8.523 distance: 227 - 228: 17.913 distance: 227 - 229: 17.747 distance: 230 - 231: 21.586 distance: 231 - 232: 33.967 distance: 231 - 234: 35.472 distance: 232 - 233: 23.873 distance: 232 - 238: 30.745 distance: 234 - 235: 33.304 distance: 235 - 236: 20.800 distance: 235 - 237: 18.042