Starting phenix.real_space_refine on Tue Nov 14 20:24:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkm_24500/11_2023/7rkm_24500_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkm_24500/11_2023/7rkm_24500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkm_24500/11_2023/7rkm_24500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkm_24500/11_2023/7rkm_24500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkm_24500/11_2023/7rkm_24500_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkm_24500/11_2023/7rkm_24500_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 72 5.16 5 C 6056 2.51 5 N 1604 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "D ASP 109": "OD1" <-> "OD2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "R TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 27": "OD1" <-> "OD2" Residue "R TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 128": "OD1" <-> "OD2" Residue "R PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 308": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 9491 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1747 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2592 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Conformer: "B" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} bond proxies already assigned to first conformer: 2622 Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "D" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "L" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 531 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 65} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PCA:plan-2': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2423 Unusual residues: {'CLR': 1} Classifications: {'peptide': 294, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 283, None: 1} Not linked: pdbres="GLU R 308 " pdbres="CLR R 401 " Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 6.12, per 1000 atoms: 0.64 Number of scatterers: 9491 At special positions: 0 Unit cell: (98.4, 134.48, 132.84, 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 72 16.00 O 1759 8.00 N 1604 7.00 C 6056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS L 8 " - pdb=" SG CYS L 34 " distance=2.04 Simple disulfide: pdb=" SG CYS L 12 " - pdb=" SG CYS L 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 173 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 2.0 seconds 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 15 sheets defined 32.3% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.312A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.917A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 30 through 42 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'L' and resid 3 through 5 No H-bonds generated for 'chain 'L' and resid 3 through 5' Processing helix chain 'L' and resid 56 through 66 removed outlier: 4.034A pdb=" N LEU L 65 " --> pdb=" O MET L 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 58 Proline residue: R 34 - end of helix removed outlier: 3.610A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 94 Proline residue: R 87 - end of helix Processing helix chain 'R' and resid 104 through 133 Processing helix chain 'R' and resid 141 through 157 removed outlier: 3.799A pdb=" N LEU R 146 " --> pdb=" O LYS R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 163 No H-bonds generated for 'chain 'R' and resid 160 through 163' Processing helix chain 'R' and resid 184 through 194 removed outlier: 4.150A pdb=" N GLU R 191 " --> pdb=" O ILE R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 217 removed outlier: 3.541A pdb=" N VAL R 217 " --> pdb=" O ARG R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 255 removed outlier: 3.787A pdb=" N VAL R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 264 through 291 Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 296 through 303 Processing sheet with id= A, first strand: chain 'A' and resid 263 through 269 Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.764A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.755A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.782A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.857A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.560A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.772A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.643A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 251 through 254 removed outlier: 6.521A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.087A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA D 40 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU D 45 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 128 through 130 Processing sheet with id= M, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.539A pdb=" N LYS D 232 " --> pdb=" O VAL D 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 214 through 219 removed outlier: 5.911A pdb=" N LEU D 166 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU D 175 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'L' and resid 48 through 51 412 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2923 1.34 - 1.46: 2284 1.46 - 1.58: 4390 1.58 - 1.71: 0 1.71 - 1.83: 100 Bond restraints: 9697 Sorted by residual: bond pdb=" N PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.345 1.463 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" CB MET B 262 " pdb=" CG MET B 262 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.88e+00 bond pdb=" C ILE R 160 " pdb=" N PRO R 161 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.96e+00 bond pdb=" SD MET B 262 " pdb=" CE MET B 262 " ideal model delta sigma weight residual 1.791 1.736 0.055 2.50e-02 1.60e+03 4.88e+00 bond pdb=" C ASN R 287 " pdb=" N PRO R 288 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.72e+00 ... (remaining 9692 not shown) Histogram of bond angle deviations from ideal: 89.71 - 98.60: 4 98.60 - 107.48: 361 107.48 - 116.36: 6112 116.36 - 125.24: 6493 125.24 - 134.12: 174 Bond angle restraints: 13144 Sorted by residual: angle pdb=" CB MET B 262 " pdb=" CG MET B 262 " pdb=" SD MET B 262 " ideal model delta sigma weight residual 112.70 89.71 22.99 3.00e+00 1.11e-01 5.87e+01 angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 131.97 -10.43 1.91e+00 2.74e-01 2.98e+01 angle pdb=" CB MET R 174 " pdb=" CG MET R 174 " pdb=" SD MET R 174 " ideal model delta sigma weight residual 112.70 125.74 -13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" N MET D 180 " pdb=" CA MET D 180 " pdb=" CB MET D 180 " ideal model delta sigma weight residual 110.49 117.48 -6.99 1.69e+00 3.50e-01 1.71e+01 angle pdb=" N ASN R 287 " pdb=" CA ASN R 287 " pdb=" C ASN R 287 " ideal model delta sigma weight residual 113.16 118.58 -5.42 1.42e+00 4.96e-01 1.46e+01 ... (remaining 13139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5360 17.94 - 35.89: 327 35.89 - 53.83: 67 53.83 - 71.77: 7 71.77 - 89.72: 4 Dihedral angle restraints: 5765 sinusoidal: 2261 harmonic: 3504 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 158.42 -65.42 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS R 23 " pdb=" SG CYS R 23 " pdb=" SG CYS R 263 " pdb=" CB CYS R 263 " ideal model delta sinusoidal sigma weight residual -86.00 -131.88 45.88 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CA ILE R 259 " pdb=" C ILE R 259 " pdb=" N SER R 260 " pdb=" CA SER R 260 " ideal model delta harmonic sigma weight residual 180.00 154.33 25.67 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 5762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1248 0.073 - 0.146: 209 0.146 - 0.219: 23 0.219 - 0.292: 9 0.292 - 0.365: 4 Chirality restraints: 1493 Sorted by residual: chirality pdb=" CA ASN R 287 " pdb=" N ASN R 287 " pdb=" C ASN R 287 " pdb=" CB ASN R 287 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB THR A 324 " pdb=" CA THR A 324 " pdb=" OG1 THR A 324 " pdb=" CG2 THR A 324 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 1490 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 57 " -0.014 2.00e-02 2.50e+03 1.69e-02 7.11e+00 pdb=" CG TRP L 57 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP L 57 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP L 57 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP L 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP L 57 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 57 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 57 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 57 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 44 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C PHE R 44 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE R 44 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU R 45 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 94 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C LEU R 94 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU R 94 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP R 95 " 0.014 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 456 2.73 - 3.27: 9413 3.27 - 3.81: 15625 3.81 - 4.36: 19400 4.36 - 4.90: 33299 Nonbonded interactions: 78193 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.181 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.199 2.440 nonbonded pdb=" OD1 ASN R 189 " pdb=" OG1 THR R 252 " model vdw 2.206 2.440 nonbonded pdb=" O LEU R 53 " pdb=" OG1 THR R 57 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.241 2.440 ... (remaining 78188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 6.970 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 29.610 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 0.005 0.118 9697 Z= 0.356 Angle : 0.970 22.986 13144 Z= 0.501 Chirality : 0.060 0.365 1493 Planarity : 0.005 0.042 1654 Dihedral : 12.310 89.718 3480 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.24), residues: 1183 helix: 0.52 (0.26), residues: 400 sheet: -1.09 (0.29), residues: 288 loop : -1.52 (0.27), residues: 495 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.079 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2440 time to fit residues: 58.8767 Evaluate side-chains 140 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9697 Z= 0.213 Angle : 0.571 7.274 13144 Z= 0.301 Chirality : 0.043 0.187 1493 Planarity : 0.003 0.037 1654 Dihedral : 4.560 26.168 1314 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.68 % Allowed : 8.78 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.81 (0.24), residues: 1183 helix: 0.94 (0.27), residues: 398 sheet: -0.96 (0.29), residues: 271 loop : -1.43 (0.26), residues: 514 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 1.247 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 147 average time/residue: 0.2425 time to fit residues: 48.5674 Evaluate side-chains 139 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1474 time to fit residues: 2.8911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 72 optimal weight: 0.0670 chunk 29 optimal weight: 0.4980 chunk 106 optimal weight: 0.3980 chunk 114 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 ASN L 45 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9697 Z= 0.157 Angle : 0.539 7.749 13144 Z= 0.282 Chirality : 0.042 0.231 1493 Planarity : 0.003 0.036 1654 Dihedral : 4.351 24.614 1314 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.25 % Allowed : 10.70 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.68 (0.24), residues: 1183 helix: 1.20 (0.27), residues: 394 sheet: -0.86 (0.28), residues: 285 loop : -1.53 (0.26), residues: 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 0.996 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 158 average time/residue: 0.2351 time to fit residues: 51.2074 Evaluate side-chains 139 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0954 time to fit residues: 2.4509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 71 optimal weight: 0.1980 chunk 106 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9697 Z= 0.204 Angle : 0.561 7.593 13144 Z= 0.292 Chirality : 0.043 0.272 1493 Planarity : 0.003 0.039 1654 Dihedral : 4.325 24.052 1314 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.16 % Allowed : 11.19 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1183 helix: 1.26 (0.27), residues: 397 sheet: -0.94 (0.28), residues: 293 loop : -1.34 (0.27), residues: 493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 147 time to evaluate : 1.090 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 154 average time/residue: 0.2308 time to fit residues: 49.0908 Evaluate side-chains 140 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0979 time to fit residues: 2.7807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.0980 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 0.3980 chunk 96 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 38 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9697 Z= 0.172 Angle : 0.537 7.731 13144 Z= 0.279 Chirality : 0.042 0.227 1493 Planarity : 0.003 0.039 1654 Dihedral : 4.236 23.937 1314 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.77 % Allowed : 12.54 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.49 (0.24), residues: 1183 helix: 1.38 (0.27), residues: 396 sheet: -0.81 (0.29), residues: 283 loop : -1.39 (0.26), residues: 504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 1.101 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 161 average time/residue: 0.2372 time to fit residues: 52.5743 Evaluate side-chains 140 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0937 time to fit residues: 2.1093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9697 Z= 0.216 Angle : 0.564 7.697 13144 Z= 0.293 Chirality : 0.042 0.235 1493 Planarity : 0.003 0.039 1654 Dihedral : 4.257 24.347 1314 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.16 % Allowed : 13.98 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.50 (0.24), residues: 1183 helix: 1.29 (0.27), residues: 400 sheet: -0.88 (0.28), residues: 294 loop : -1.29 (0.27), residues: 489 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.125 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 151 average time/residue: 0.2439 time to fit residues: 50.5107 Evaluate side-chains 141 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0936 time to fit residues: 2.6441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9697 Z= 0.209 Angle : 0.556 7.673 13144 Z= 0.290 Chirality : 0.042 0.197 1493 Planarity : 0.003 0.039 1654 Dihedral : 4.255 24.097 1314 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.58 % Allowed : 14.46 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.45 (0.24), residues: 1183 helix: 1.37 (0.27), residues: 396 sheet: -0.84 (0.28), residues: 294 loop : -1.30 (0.27), residues: 493 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 1.167 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 145 average time/residue: 0.2594 time to fit residues: 51.4367 Evaluate side-chains 141 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 1.119 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0894 time to fit residues: 2.2145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 0.0770 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.1980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9697 Z= 0.174 Angle : 0.552 7.854 13144 Z= 0.287 Chirality : 0.041 0.202 1493 Planarity : 0.003 0.038 1654 Dihedral : 4.207 23.937 1314 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.29 % Allowed : 15.24 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.42 (0.24), residues: 1183 helix: 1.32 (0.27), residues: 403 sheet: -0.70 (0.29), residues: 283 loop : -1.32 (0.26), residues: 497 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 147 time to evaluate : 1.154 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 150 average time/residue: 0.2533 time to fit residues: 51.3084 Evaluate side-chains 142 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0886 time to fit residues: 1.6834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.0998 > 50: distance: 57 - 61: 33.892 distance: 62 - 63: 56.976 distance: 62 - 65: 55.531 distance: 63 - 64: 40.417 distance: 63 - 69: 57.021 distance: 65 - 66: 44.898 distance: 66 - 67: 47.075 distance: 69 - 70: 39.259 distance: 70 - 73: 39.224 distance: 71 - 72: 38.868 distance: 71 - 76: 39.490 distance: 73 - 74: 56.287 distance: 73 - 75: 56.139 distance: 77 - 78: 39.752 distance: 78 - 79: 39.244 distance: 78 - 84: 57.241 distance: 80 - 81: 39.948 distance: 81 - 82: 38.848 distance: 81 - 83: 57.383 distance: 85 - 86: 39.767 distance: 85 - 88: 39.732 distance: 86 - 87: 39.339 distance: 89 - 90: 24.746 distance: 89 - 91: 41.346 distance: 90 - 92: 46.163 distance: 91 - 93: 40.762 distance: 92 - 94: 56.917 distance: 93 - 94: 35.157 distance: 94 - 95: 52.733 distance: 97 - 98: 56.887 distance: 97 - 100: 55.429 distance: 98 - 99: 56.536 distance: 98 - 104: 39.906 distance: 100 - 101: 55.393 distance: 101 - 103: 56.650 distance: 104 - 105: 38.974 distance: 105 - 108: 40.777 distance: 108 - 109: 38.897 distance: 109 - 110: 39.652 distance: 109 - 111: 41.205 distance: 110 - 112: 39.703 distance: 111 - 113: 41.062 distance: 112 - 114: 40.176 distance: 113 - 114: 39.034 distance: 116 - 117: 38.622 distance: 117 - 120: 40.755 distance: 118 - 119: 56.038 distance: 120 - 121: 40.462 distance: 121 - 122: 63.126 distance: 121 - 123: 56.427 distance: 125 - 128: 40.400 distance: 126 - 127: 39.687 distance: 128 - 129: 56.035 distance: 130 - 131: 57.277 distance: 130 - 132: 55.537 distance: 133 - 134: 13.131 distance: 134 - 135: 12.004 distance: 134 - 137: 47.208 distance: 135 - 136: 57.009 distance: 135 - 140: 39.696 distance: 137 - 139: 39.251 distance: 141 - 142: 39.386 distance: 141 - 144: 40.229 distance: 142 - 143: 39.907 distance: 142 - 146: 33.477 distance: 144 - 145: 57.143