Starting phenix.real_space_refine on Fri Oct 11 20:41:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ied_35380/10_2024/8ied_35380.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ied_35380/10_2024/8ied_35380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ied_35380/10_2024/8ied_35380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ied_35380/10_2024/8ied_35380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ied_35380/10_2024/8ied_35380.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ied_35380/10_2024/8ied_35380.cif" } resolution = 3.33 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= 0.111 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 79 5.16 5 C 6888 2.51 5 N 1770 2.21 5 O 1955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 10694 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2062 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2250 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 1 Chain: "C" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1659 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2527 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "N" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1707 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "Y" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 385 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 7.26, per 1000 atoms: 0.68 Number of scatterers: 10694 At special positions: 0 Unit cell: (94.77, 119.88, 144.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 P 2 15.00 O 1955 8.00 N 1770 7.00 C 6888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS N 147 " - pdb=" SG CYS N 217 " distance=2.03 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: 2.49 Conformation dependent library (CDL) restraints added in 1.4 seconds 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2594 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 41.9% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 46 through 74 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 84 through 105 removed outlier: 3.540A pdb=" N ASN A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 151 Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 161 through 187 removed outlier: 3.645A pdb=" N LEU A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 187 " --> pdb=" O TRP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 246 removed outlier: 3.848A pdb=" N TRP A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 280 Processing helix chain 'A' and resid 284 through 317 Proline residue: A 310 - end of helix removed outlier: 3.660A pdb=" N ALA A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 74 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 84 through 105 removed outlier: 3.543A pdb=" N VAL B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 150 removed outlier: 3.870A pdb=" N MET B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 161 through 187 removed outlier: 3.755A pdb=" N LEU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 246 removed outlier: 3.535A pdb=" N TRP B 224 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 281 Processing helix chain 'B' and resid 284 through 315 Proline residue: B 310 - end of helix Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.552A pdb=" N ARG B 327 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 96 through 102 removed outlier: 3.563A pdb=" N GLU C 101 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP C 102 " --> pdb=" O CYS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 130 through 135 removed outlier: 6.292A pdb=" N PHE C 133 " --> pdb=" O ASN C 130 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C 135 " --> pdb=" O LYS C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 153 Processing helix chain 'C' and resid 170 through 184 Processing helix chain 'C' and resid 205 through 225 Processing helix chain 'D' and resid 4 through 25 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.581A pdb=" N SER N 31 " --> pdb=" O ALA N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.722A pdb=" N GLY N 56 " --> pdb=" O SER N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.699A pdb=" N ASP N 90 " --> pdb=" O THR N 87 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR N 91 " --> pdb=" O SER N 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 87 through 91' Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.504A pdb=" N MET Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU Y 22 " --> pdb=" O GLN Y 18 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 34 through 44 removed outlier: 3.592A pdb=" N MET Y 38 " --> pdb=" O ALA Y 34 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU Y 42 " --> pdb=" O MET Y 38 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 216 removed outlier: 4.040A pdb=" N PHE A 215 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 192 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 195 " --> pdb=" O MET B 199 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 195 " --> pdb=" O MET A 199 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 201 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 193 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 190 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 215 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.987A pdb=" N ALA C 105 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE C 139 " --> pdb=" O TYR C 194 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N HIS C 196 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU C 141 " --> pdb=" O HIS C 196 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.750A pdb=" N VAL D 327 " --> pdb=" O TRP D 339 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.561A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA D 73 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.988A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY D 116 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE D 120 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 151 removed outlier: 6.648A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE D 151 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLN D 156 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS D 166 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 191 through 192 removed outlier: 4.021A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N THR D 221 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU D 210 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.578A pdb=" N CYS D 233 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 245 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS D 250 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 276 through 278 removed outlier: 3.583A pdb=" N LEU D 285 " --> pdb=" O TRP D 297 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.822A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.822A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE N 110 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 142 through 147 removed outlier: 3.871A pdb=" N PHE N 200 " --> pdb=" O CYS N 147 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER N 192 " --> pdb=" O THR N 203 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 182 through 183 removed outlier: 6.529A pdb=" N TRP N 164 " --> pdb=" O LEU N 176 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1695 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: 3.61 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1677 1.32 - 1.44: 2970 1.44 - 1.57: 6149 1.57 - 1.70: 4 1.70 - 1.83: 112 Bond restraints: 10912 Sorted by residual: bond pdb=" C39 PC1 A 601 " pdb=" C3A PC1 A 601 " ideal model delta sigma weight residual 1.524 1.318 0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C39 PC1 B 601 " pdb=" C3A PC1 B 601 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C31 PC1 B 601 " pdb=" O31 PC1 B 601 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C31 PC1 A 601 " pdb=" O31 PC1 A 601 " ideal model delta sigma weight residual 1.330 1.418 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C2 PC1 B 601 " pdb=" O21 PC1 B 601 " ideal model delta sigma weight residual 1.430 1.380 0.050 2.00e-02 2.50e+03 6.19e+00 ... (remaining 10907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 14651 2.98 - 5.95: 136 5.95 - 8.93: 28 8.93 - 11.91: 1 11.91 - 14.89: 2 Bond angle restraints: 14818 Sorted by residual: angle pdb=" O12 PC1 B 601 " pdb=" P PC1 B 601 " pdb=" O14 PC1 B 601 " ideal model delta sigma weight residual 123.67 108.78 14.89 3.00e+00 1.11e-01 2.46e+01 angle pdb=" O12 PC1 A 601 " pdb=" P PC1 A 601 " pdb=" O14 PC1 A 601 " ideal model delta sigma weight residual 123.67 109.52 14.15 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C PRO C 157 " pdb=" N LEU C 158 " pdb=" CA LEU C 158 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C ASP C 85 " pdb=" N VAL C 86 " pdb=" CA VAL C 86 " ideal model delta sigma weight residual 121.97 129.03 -7.06 1.80e+00 3.09e-01 1.54e+01 angle pdb=" N PRO A 252 " pdb=" CA PRO A 252 " pdb=" C PRO A 252 " ideal model delta sigma weight residual 110.70 114.71 -4.01 1.22e+00 6.72e-01 1.08e+01 ... (remaining 14813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5821 17.72 - 35.43: 495 35.43 - 53.15: 98 53.15 - 70.86: 16 70.86 - 88.58: 12 Dihedral angle restraints: 6442 sinusoidal: 2419 harmonic: 4023 Sorted by residual: dihedral pdb=" CB CYS N 147 " pdb=" SG CYS N 147 " pdb=" SG CYS N 217 " pdb=" CB CYS N 217 " ideal model delta sinusoidal sigma weight residual 93.00 -178.42 -88.58 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CA GLN N 130 " pdb=" C GLN N 130 " pdb=" N ALA N 131 " pdb=" CA ALA N 131 " ideal model delta harmonic sigma weight residual 180.00 159.33 20.67 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ILE B 307 " pdb=" C ILE B 307 " pdb=" N PHE B 308 " pdb=" CA PHE B 308 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 6439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1523 0.071 - 0.141: 217 0.141 - 0.212: 6 0.212 - 0.283: 2 0.283 - 0.353: 1 Chirality restraints: 1749 Sorted by residual: chirality pdb=" CB VAL C 86 " pdb=" CA VAL C 86 " pdb=" CG1 VAL C 86 " pdb=" CG2 VAL C 86 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CB ILE A 189 " pdb=" CA ILE A 189 " pdb=" CG1 ILE A 189 " pdb=" CG2 ILE A 189 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1746 not shown) Planarity restraints: 1829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 252 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO B 253 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 253 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 253 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 252 " -0.044 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO A 253 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 235 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO D 236 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 236 " -0.029 5.00e-02 4.00e+02 ... (remaining 1826 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 379 2.71 - 3.26: 10148 3.26 - 3.81: 17525 3.81 - 4.35: 20751 4.35 - 4.90: 36604 Nonbonded interactions: 85407 Sorted by model distance: nonbonded pdb=" OE2 GLU D 260 " pdb=" OG1 THR D 263 " model vdw 2.166 3.040 nonbonded pdb=" O VAL A 298 " pdb=" OG1 THR A 302 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR C 194 " pdb=" OD2 ASP C 215 " model vdw 2.238 3.040 nonbonded pdb=" OG SER N 149 " pdb=" O LYS N 151 " model vdw 2.247 3.040 nonbonded pdb=" O TYR B 146 " pdb=" OG1 THR B 150 " model vdw 2.254 3.040 ... (remaining 85402 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' and (resid 44 through 110 or resid 115 through 318 or resid 601)) selection = (chain 'B' and (resid 44 through 110 or resid 115 through 150 or (resid 151 thro \ ugh 152 and (name N or name CA or name C or name O or name CB )) or resid 153 th \ rough 154 or (resid 155 and (name N or name CA or name C or name O or name CB )) \ or resid 159 through 318 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.110 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.206 10912 Z= 0.416 Angle : 0.771 14.886 14818 Z= 0.381 Chirality : 0.048 0.353 1749 Planarity : 0.005 0.069 1829 Dihedral : 14.177 85.674 3839 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.22), residues: 1374 helix: 1.10 (0.21), residues: 536 sheet: -0.52 (0.31), residues: 311 loop : -1.64 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 229 HIS 0.006 0.001 HIS N 220 PHE 0.023 0.002 PHE A 306 TYR 0.022 0.002 TYR N 223 ARG 0.004 0.000 ARG B 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 LYS cc_start: 0.8194 (tttp) cc_final: 0.7651 (ttpt) REVERT: B 125 SER cc_start: 0.9036 (t) cc_final: 0.8750 (p) REVERT: B 261 MET cc_start: 0.7754 (mmm) cc_final: 0.7458 (mmm) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2289 time to fit residues: 87.0880 Evaluate side-chains 175 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.0870 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 0.0970 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN D 225 HIS D 237 ASN N 77 ASN N 130 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10912 Z= 0.269 Angle : 0.607 8.743 14818 Z= 0.320 Chirality : 0.044 0.189 1749 Planarity : 0.005 0.060 1829 Dihedral : 8.905 72.395 1572 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.76 % Allowed : 9.04 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1374 helix: 2.15 (0.22), residues: 542 sheet: -0.28 (0.31), residues: 303 loop : -1.46 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 211 HIS 0.004 0.001 HIS N 35 PHE 0.022 0.002 PHE B 66 TYR 0.029 0.002 TYR N 60 ARG 0.007 0.001 ARG D 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7099 (ptm) cc_final: 0.6805 (ppp) REVERT: B 81 LYS cc_start: 0.8117 (tttp) cc_final: 0.7613 (ttpt) REVERT: C 136 ASP cc_start: 0.7859 (t70) cc_final: 0.7602 (t0) REVERT: D 65 THR cc_start: 0.7244 (p) cc_final: 0.6838 (t) REVERT: D 130 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7231 (mp0) REVERT: D 156 GLN cc_start: 0.7659 (mt0) cc_final: 0.7422 (mt0) REVERT: N 72 ARG cc_start: 0.5626 (ptm160) cc_final: 0.5045 (ptm160) REVERT: Y 38 MET cc_start: 0.5655 (mmm) cc_final: 0.5297 (ptt) outliers start: 20 outliers final: 14 residues processed: 211 average time/residue: 0.2272 time to fit residues: 67.8377 Evaluate side-chains 190 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 176 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 133 optimal weight: 0.0170 chunk 110 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10912 Z= 0.263 Angle : 0.586 6.588 14818 Z= 0.312 Chirality : 0.044 0.194 1749 Planarity : 0.005 0.066 1829 Dihedral : 8.544 73.420 1572 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.19 % Allowed : 11.94 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.24), residues: 1374 helix: 2.39 (0.22), residues: 545 sheet: -0.24 (0.31), residues: 303 loop : -1.46 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 211 HIS 0.005 0.001 HIS D 225 PHE 0.018 0.002 PHE A 70 TYR 0.021 0.002 TYR N 223 ARG 0.006 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 195 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7129 (ptm) cc_final: 0.6853 (ppp) REVERT: C 136 ASP cc_start: 0.8025 (t70) cc_final: 0.7723 (t0) REVERT: D 130 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7314 (mp0) REVERT: D 283 ARG cc_start: 0.6336 (mmm160) cc_final: 0.5860 (mmm160) REVERT: D 339 TRP cc_start: 0.6571 (m100) cc_final: 0.5937 (m100) REVERT: N 64 VAL cc_start: 0.4090 (t) cc_final: 0.3828 (m) outliers start: 25 outliers final: 18 residues processed: 208 average time/residue: 0.1825 time to fit residues: 53.0241 Evaluate side-chains 191 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 ASN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10912 Z= 0.236 Angle : 0.563 8.029 14818 Z= 0.300 Chirality : 0.043 0.212 1749 Planarity : 0.004 0.064 1829 Dihedral : 8.111 70.373 1572 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.46 % Allowed : 13.26 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.24), residues: 1374 helix: 2.37 (0.22), residues: 547 sheet: -0.43 (0.32), residues: 298 loop : -1.50 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 211 HIS 0.005 0.001 HIS D 225 PHE 0.016 0.001 PHE A 70 TYR 0.022 0.002 TYR N 223 ARG 0.004 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6861 (mm) REVERT: A 174 MET cc_start: 0.7077 (ptm) cc_final: 0.6785 (ppp) REVERT: B 81 LYS cc_start: 0.7972 (ttmm) cc_final: 0.7266 (ttpt) REVERT: B 200 THR cc_start: 0.5898 (OUTLIER) cc_final: 0.5536 (p) REVERT: C 136 ASP cc_start: 0.8070 (t70) cc_final: 0.7735 (t0) REVERT: D 130 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7310 (mp0) REVERT: D 155 ASN cc_start: 0.7722 (t0) cc_final: 0.7338 (t0) REVERT: D 262 MET cc_start: 0.5086 (tpp) cc_final: 0.4497 (tpp) REVERT: D 283 ARG cc_start: 0.6223 (mmm160) cc_final: 0.5719 (mmm160) REVERT: D 339 TRP cc_start: 0.6499 (m100) cc_final: 0.5851 (m100) REVERT: Y 21 MET cc_start: 0.6732 (tpp) cc_final: 0.6405 (tmm) outliers start: 28 outliers final: 15 residues processed: 204 average time/residue: 0.2096 time to fit residues: 60.9226 Evaluate side-chains 187 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS C 181 GLN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10912 Z= 0.256 Angle : 0.573 6.757 14818 Z= 0.304 Chirality : 0.043 0.219 1749 Planarity : 0.004 0.064 1829 Dihedral : 7.926 70.619 1572 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.07 % Allowed : 14.14 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1374 helix: 2.35 (0.22), residues: 546 sheet: -0.51 (0.32), residues: 292 loop : -1.53 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 211 HIS 0.003 0.001 HIS C 80 PHE 0.018 0.001 PHE A 70 TYR 0.022 0.002 TYR N 223 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 177 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6908 (mm) REVERT: A 174 MET cc_start: 0.7103 (ptm) cc_final: 0.6773 (ppp) REVERT: B 81 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7256 (ttpt) REVERT: B 200 THR cc_start: 0.5777 (OUTLIER) cc_final: 0.5357 (p) REVERT: C 35 LYS cc_start: 0.8010 (mtmm) cc_final: 0.7762 (mttp) REVERT: C 136 ASP cc_start: 0.8152 (t70) cc_final: 0.7798 (t0) REVERT: D 130 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7359 (mp0) REVERT: D 155 ASN cc_start: 0.7633 (t0) cc_final: 0.7399 (t0) REVERT: D 339 TRP cc_start: 0.6610 (m100) cc_final: 0.5968 (m100) REVERT: Y 21 MET cc_start: 0.6702 (tpp) cc_final: 0.6412 (tmm) REVERT: Y 38 MET cc_start: 0.7203 (pmm) cc_final: 0.6882 (pmm) outliers start: 35 outliers final: 22 residues processed: 198 average time/residue: 0.2205 time to fit residues: 62.8560 Evaluate side-chains 193 residues out of total 1206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.0050 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: