Starting phenix.real_space_refine on Mon Mar 11 13:20:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzq_27805/03_2024/8dzq_27805_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzq_27805/03_2024/8dzq_27805.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzq_27805/03_2024/8dzq_27805_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzq_27805/03_2024/8dzq_27805_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzq_27805/03_2024/8dzq_27805_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzq_27805/03_2024/8dzq_27805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzq_27805/03_2024/8dzq_27805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzq_27805/03_2024/8dzq_27805_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzq_27805/03_2024/8dzq_27805_updated.pdb" } resolution = 2.82 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= 0.001 sd= 0.021 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 58 5.16 5 C 5337 2.51 5 N 1397 2.21 5 O 1550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8342 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2484 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 292 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1770 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Chain: "B" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1648 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 2148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2148 Unusual residues: {'U99': 1} Classifications: {'peptide': 274, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 8, 'TRANS': 265, None: 1} Not linked: pdbres="ARG A 339 " pdbres="U99 A 401 " Chain breaks: 3 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 47 Time building chain proxies: 4.73, per 1000 atoms: 0.57 Number of scatterers: 8342 At special positions: 0 Unit cell: (90.64, 121.44, 127.6, 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 58 16.00 O 1550 8.00 N 1397 7.00 C 5337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 210 " 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: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 31.7% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'C' and resid 6 through 24 Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'B' and resid 7 through 32 removed outlier: 4.271A pdb=" N LYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 252 through 255 No H-bonds generated for 'chain 'B' and resid 252 through 255' Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 297 through 311 removed outlier: 4.342A pdb=" N ALA B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 350 Processing helix chain 'A' and resid 58 through 86 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 128 through 161 Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.981A pdb=" N PHE A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.869A pdb=" N VAL A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 234 Processing helix chain 'A' and resid 236 through 255 removed outlier: 4.289A pdb=" N SER A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 298 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 307 through 330 removed outlier: 3.720A pdb=" N TYR A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing sheet with id= A, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.981A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.098A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.863A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 198 through 202 removed outlier: 6.533A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.803A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.581A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.786A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.556A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.242A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 143 through 147 Processing sheet with id= L, first strand: chain 'B' and resid 319 through 323 removed outlier: 6.804A pdb=" N ILE B 265 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N HIS B 322 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B 267 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 221 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N HIS B 196 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU B 36 " --> pdb=" O HIS B 196 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ARG B 198 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU B 38 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE B 200 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 198 through 200 388 hydrogen bonds defined for protein. 1101 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: 2.46 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1566 1.33 - 1.45: 2172 1.45 - 1.57: 4689 1.57 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 8510 Sorted by residual: bond pdb=" C20 U99 A 401 " pdb=" C22 U99 A 401 " ideal model delta sigma weight residual 0.452 1.563 -1.111 2.00e-02 2.50e+03 3.08e+03 bond pdb=" C10 U99 A 401 " pdb=" C11 U99 A 401 " ideal model delta sigma weight residual 0.683 1.528 -0.845 2.00e-02 2.50e+03 1.78e+03 bond pdb=" C10 U99 A 401 " pdb=" C8 U99 A 401 " ideal model delta sigma weight residual 0.980 1.539 -0.559 2.00e-02 2.50e+03 7.81e+02 bond pdb=" C5 U99 A 401 " pdb=" C8 U99 A 401 " ideal model delta sigma weight residual 1.134 1.564 -0.430 2.00e-02 2.50e+03 4.62e+02 bond pdb=" C12 U99 A 401 " pdb=" C20 U99 A 401 " ideal model delta sigma weight residual 1.181 1.551 -0.370 2.00e-02 2.50e+03 3.42e+02 ... (remaining 8505 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.58: 123 105.58 - 112.73: 4572 112.73 - 119.87: 2784 119.87 - 127.02: 3990 127.02 - 134.17: 96 Bond angle restraints: 11565 Sorted by residual: angle pdb=" N VAL B 202 " pdb=" CA VAL B 202 " pdb=" C VAL B 202 " ideal model delta sigma weight residual 111.88 106.75 5.13 1.06e+00 8.90e-01 2.34e+01 angle pdb=" C ASN B 295 " pdb=" N THR B 296 " pdb=" CA THR B 296 " ideal model delta sigma weight residual 121.54 130.43 -8.89 1.91e+00 2.74e-01 2.17e+01 angle pdb=" N ARG C 68 " pdb=" CA ARG C 68 " pdb=" C ARG C 68 " ideal model delta sigma weight residual 114.56 109.40 5.16 1.27e+00 6.20e-01 1.65e+01 angle pdb=" C ASN A 122 " pdb=" N SER A 123 " pdb=" CA SER A 123 " ideal model delta sigma weight residual 121.54 114.59 6.95 1.91e+00 2.74e-01 1.32e+01 angle pdb=" N ILE C 37 " pdb=" CA ILE C 37 " pdb=" C ILE C 37 " ideal model delta sigma weight residual 112.98 108.49 4.49 1.25e+00 6.40e-01 1.29e+01 ... (remaining 11560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.94: 4618 19.94 - 39.88: 345 39.88 - 59.81: 29 59.81 - 79.75: 6 79.75 - 99.69: 4 Dihedral angle restraints: 5002 sinusoidal: 1816 harmonic: 3186 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 210 " pdb=" CB CYS A 210 " ideal model delta sinusoidal sigma weight residual -86.00 -165.52 79.52 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" CA LEU B 199 " pdb=" C LEU B 199 " pdb=" N PHE B 200 " pdb=" CA PHE B 200 " ideal model delta harmonic sigma weight residual 180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA LYS C 78 " pdb=" C LYS C 78 " pdb=" N LEU C 79 " pdb=" CA LEU C 79 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 4999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.508: 1358 0.508 - 1.017: 1 1.017 - 1.525: 1 1.525 - 2.033: 1 2.033 - 2.542: 1 Chirality restraints: 1362 Sorted by residual: chirality pdb=" C20 U99 A 401 " pdb=" C12 U99 A 401 " pdb=" C19 U99 A 401 " pdb=" C22 U99 A 401 " both_signs ideal model delta sigma weight residual False 0.50 3.04 -2.54 2.00e-01 2.50e+01 1.61e+02 chirality pdb=" C8 U99 A 401 " pdb=" C10 U99 A 401 " pdb=" C22 U99 A 401 " pdb=" C5 U99 A 401 " both_signs ideal model delta sigma weight residual False 1.13 3.00 -1.88 2.00e-01 2.50e+01 8.79e+01 chirality pdb=" C22 U99 A 401 " pdb=" C20 U99 A 401 " pdb=" C23 U99 A 401 " pdb=" C8 U99 A 401 " both_signs ideal model delta sigma weight residual False -0.67 -1.93 1.26 2.00e-01 2.50e+01 3.97e+01 ... (remaining 1359 not shown) Planarity restraints: 1445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 137 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C ARG C 137 " 0.043 2.00e-02 2.50e+03 pdb=" O ARG C 137 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU C 138 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 165 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C PHE E 165 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE E 165 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU E 166 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 246 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C ALA B 246 " -0.034 2.00e-02 2.50e+03 pdb=" O ALA B 246 " 0.013 2.00e-02 2.50e+03 pdb=" N SER B 247 " 0.011 2.00e-02 2.50e+03 ... (remaining 1442 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1641 2.78 - 3.31: 7723 3.31 - 3.84: 13766 3.84 - 4.37: 15972 4.37 - 4.90: 28139 Nonbonded interactions: 67241 Sorted by model distance: nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.244 2.440 nonbonded pdb=" O GLY E 8 " pdb=" OG1 THR E 115 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.263 2.440 nonbonded pdb=" OD2 ASP C 186 " pdb=" OG SER B 207 " model vdw 2.295 2.440 nonbonded pdb=" O ALA C 231 " pdb=" OG1 THR C 243 " model vdw 2.309 2.440 ... (remaining 67236 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.300 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.900 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 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 : 0.019 1.111 8510 Z= 1.389 Angle : 0.793 10.042 11565 Z= 0.405 Chirality : 0.106 2.542 1362 Planarity : 0.004 0.043 1445 Dihedral : 13.383 99.689 2936 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.46 (0.25), residues: 1072 helix: 1.13 (0.27), residues: 355 sheet: -0.04 (0.30), residues: 276 loop : -1.68 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 164 HIS 0.017 0.002 HIS E 155 PHE 0.019 0.002 PHE C 278 TYR 0.023 0.002 TYR A 140 ARG 0.008 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: E 95 TYR cc_start: 0.6503 (m-10) cc_final: 0.6295 (m-10) REVERT: A 228 ILE cc_start: 0.7726 (mm) cc_final: 0.7472 (mm) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.8167 time to fit residues: 148.0426 Evaluate side-chains 150 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.0770 chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.0970 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 230 ASN C 293 ASN E 219 GLN B 233 GLN A 122 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 8510 Z= 0.287 Angle : 0.663 16.668 11565 Z= 0.319 Chirality : 0.047 0.515 1362 Planarity : 0.004 0.033 1445 Dihedral : 5.438 85.428 1187 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.60 % Allowed : 11.57 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.15 (0.26), residues: 1072 helix: 1.69 (0.28), residues: 354 sheet: -0.10 (0.30), residues: 279 loop : -1.62 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 169 HIS 0.004 0.001 HIS B 189 PHE 0.023 0.002 PHE B 200 TYR 0.019 0.002 TYR A 140 ARG 0.008 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: C 217 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6344 (pmt) REVERT: E 208 GLU cc_start: 0.6864 (mp0) cc_final: 0.6557 (mp0) REVERT: A 228 ILE cc_start: 0.7755 (mm) cc_final: 0.7521 (mm) outliers start: 14 outliers final: 0 residues processed: 157 average time/residue: 0.9293 time to fit residues: 157.7334 Evaluate side-chains 141 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 217 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN C 293 ASN E 219 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 8510 Z= 0.314 Angle : 0.655 16.986 11565 Z= 0.316 Chirality : 0.046 0.449 1362 Planarity : 0.003 0.031 1445 Dihedral : 5.390 84.992 1187 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.72 % Allowed : 15.35 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.12 (0.26), residues: 1072 helix: 1.80 (0.28), residues: 354 sheet: -0.14 (0.30), residues: 282 loop : -1.65 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 169 HIS 0.005 0.001 HIS B 189 PHE 0.019 0.002 PHE B 200 TYR 0.017 0.002 TYR A 140 ARG 0.005 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: C 217 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.6308 (pmt) REVERT: E 180 MET cc_start: 0.4705 (ttp) cc_final: 0.4425 (ttp) REVERT: E 208 GLU cc_start: 0.6956 (mp0) cc_final: 0.6635 (mp0) REVERT: B 309 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: A 107 LEU cc_start: 0.8030 (mt) cc_final: 0.7782 (mp) REVERT: A 228 ILE cc_start: 0.7812 (mm) cc_final: 0.7570 (OUTLIER) REVERT: A 332 PHE cc_start: 0.7768 (m-80) cc_final: 0.7446 (m-80) outliers start: 15 outliers final: 4 residues processed: 155 average time/residue: 0.9633 time to fit residues: 161.3010 Evaluate side-chains 151 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 50 optimal weight: 0.0030 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 0.0370 chunk 98 optimal weight: 0.0040 chunk 104 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 28 optimal weight: 0.0270 overall best weight: 0.1338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 ASN E 219 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN A 322 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.156 8510 Z= 0.247 Angle : 0.612 16.843 11565 Z= 0.290 Chirality : 0.044 0.458 1362 Planarity : 0.003 0.029 1445 Dihedral : 5.135 86.283 1187 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.06 % Allowed : 16.27 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.10 (0.26), residues: 1072 helix: 2.02 (0.28), residues: 357 sheet: -0.04 (0.30), residues: 276 loop : -1.56 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 169 HIS 0.002 0.000 HIS A 291 PHE 0.013 0.001 PHE B 200 TYR 0.020 0.001 TYR A 140 ARG 0.005 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: E 208 GLU cc_start: 0.6881 (mp0) cc_final: 0.6549 (mp0) REVERT: B 198 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6734 (ptt90) REVERT: B 309 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: A 107 LEU cc_start: 0.7961 (mt) cc_final: 0.7741 (mp) REVERT: A 228 ILE cc_start: 0.7738 (mm) cc_final: 0.7533 (mm) REVERT: A 249 MET cc_start: 0.7302 (ttt) cc_final: 0.6783 (ttt) REVERT: A 332 PHE cc_start: 0.7776 (m-80) cc_final: 0.7395 (m-80) outliers start: 18 outliers final: 2 residues processed: 159 average time/residue: 0.8880 time to fit residues: 153.2890 Evaluate side-chains 144 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 0.0050 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 0.0670 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.4932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 230 ASN E 219 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 8510 Z= 0.285 Angle : 0.632 17.038 11565 Z= 0.302 Chirality : 0.045 0.459 1362 Planarity : 0.003 0.028 1445 Dihedral : 5.152 85.163 1187 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.52 % Allowed : 17.98 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1072 helix: 1.99 (0.28), residues: 357 sheet: -0.15 (0.30), residues: 281 loop : -1.56 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 169 HIS 0.004 0.001 HIS B 189 PHE 0.019 0.001 PHE B 200 TYR 0.019 0.002 TYR A 140 ARG 0.006 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: C 217 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6373 (pmt) REVERT: E 208 GLU cc_start: 0.6960 (mp0) cc_final: 0.6654 (mp0) REVERT: B 198 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7126 (ptt90) REVERT: B 309 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: A 107 LEU cc_start: 0.7983 (mt) cc_final: 0.7766 (mp) REVERT: A 228 ILE cc_start: 0.7787 (mm) cc_final: 0.7572 (mm) REVERT: A 332 PHE cc_start: 0.7819 (m-80) cc_final: 0.7430 (m-80) outliers start: 22 outliers final: 7 residues processed: 163 average time/residue: 0.8966 time to fit residues: 158.4605 Evaluate side-chains 161 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 86 optimal weight: 0.0070 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN E 219 GLN ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 8510 Z= 0.323 Angle : 0.659 17.027 11565 Z= 0.317 Chirality : 0.046 0.457 1362 Planarity : 0.003 0.029 1445 Dihedral : 5.286 82.706 1187 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.09 % Allowed : 18.10 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1072 helix: 1.87 (0.28), residues: 356 sheet: -0.14 (0.30), residues: 276 loop : -1.59 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.004 0.001 HIS E 220 PHE 0.020 0.002 PHE B 200 TYR 0.021 0.002 TYR E 178 ARG 0.007 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 0.884 Fit side-chains REVERT: C 217 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6337 (pmt) REVERT: E 206 ARG cc_start: 0.6473 (mmp80) cc_final: 0.6070 (mmp80) REVERT: E 208 GLU cc_start: 0.7000 (mp0) cc_final: 0.6667 (mp0) REVERT: B 198 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6774 (ptt180) REVERT: B 309 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: A 107 LEU cc_start: 0.8005 (mt) cc_final: 0.7749 (mp) REVERT: A 228 ILE cc_start: 0.7861 (mm) cc_final: 0.7651 (mm) REVERT: A 332 PHE cc_start: 0.7846 (m-80) cc_final: 0.7506 (m-80) outliers start: 27 outliers final: 11 residues processed: 166 average time/residue: 0.9334 time to fit residues: 167.4812 Evaluate side-chains 160 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 256 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN E 219 GLN A 122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 8510 Z= 0.333 Angle : 0.673 17.029 11565 Z= 0.324 Chirality : 0.046 0.456 1362 Planarity : 0.004 0.078 1445 Dihedral : 5.317 81.411 1187 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.32 % Allowed : 19.01 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.10 (0.26), residues: 1072 helix: 1.80 (0.28), residues: 356 sheet: -0.09 (0.31), residues: 272 loop : -1.64 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.005 0.001 HIS B 189 PHE 0.022 0.002 PHE B 200 TYR 0.019 0.002 TYR A 140 ARG 0.006 0.000 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 0.885 Fit side-chains REVERT: C 217 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6333 (pmt) REVERT: E 206 ARG cc_start: 0.6504 (mmp80) cc_final: 0.6111 (mmp80) REVERT: E 208 GLU cc_start: 0.6995 (mp0) cc_final: 0.6653 (mp0) REVERT: B 198 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6778 (ptt180) REVERT: B 309 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6530 (mp0) REVERT: A 107 LEU cc_start: 0.7953 (mt) cc_final: 0.7655 (mp) REVERT: A 332 PHE cc_start: 0.7887 (m-80) cc_final: 0.7570 (m-80) outliers start: 29 outliers final: 16 residues processed: 166 average time/residue: 0.9272 time to fit residues: 166.5741 Evaluate side-chains 167 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 323 ASP Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 311 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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-dev-5265/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: 51.4473 > 50: distance: 5 - 20: 3.535 distance: 9 - 29: 12.786 distance: 13 - 34: 11.118 distance: 16 - 20: 4.281 distance: 17 - 39: 21.726 distance: 20 - 21: 4.758 distance: 21 - 22: 6.046 distance: 21 - 24: 5.077 distance: 22 - 23: 4.958 distance: 22 - 29: 12.959 distance: 23 - 43: 9.014 distance: 24 - 25: 9.630 distance: 25 - 26: 3.564 distance: 26 - 27: 8.518 distance: 27 - 28: 11.108 distance: 29 - 30: 6.489 distance: 30 - 31: 10.873 distance: 30 - 33: 13.260 distance: 31 - 32: 9.398 distance: 31 - 34: 7.258 distance: 32 - 51: 19.317 distance: 34 - 35: 6.861 distance: 35 - 36: 6.284 distance: 35 - 38: 10.312 distance: 36 - 37: 12.541 distance: 36 - 39: 17.058 distance: 37 - 57: 33.939 distance: 39 - 40: 20.943 distance: 40 - 41: 21.146 distance: 41 - 42: 28.961 distance: 41 - 43: 22.529 distance: 42 - 62: 24.097 distance: 43 - 44: 11.561 distance: 44 - 45: 17.112 distance: 44 - 47: 3.153 distance: 45 - 46: 7.535 distance: 45 - 51: 21.419 distance: 47 - 48: 8.747 distance: 48 - 50: 5.833 distance: 51 - 52: 8.103 distance: 52 - 53: 12.938 distance: 52 - 55: 8.313 distance: 53 - 54: 10.749 distance: 53 - 57: 35.320 distance: 55 - 56: 10.532 distance: 57 - 58: 42.091 distance: 58 - 59: 21.812 distance: 58 - 61: 13.009 distance: 59 - 60: 13.801 distance: 59 - 62: 11.834 distance: 62 - 63: 12.621 distance: 63 - 64: 4.195 distance: 63 - 66: 18.444 distance: 64 - 65: 32.023 distance: 64 - 67: 13.685 distance: 67 - 68: 8.201 distance: 68 - 69: 11.723 distance: 68 - 71: 10.688 distance: 69 - 70: 7.493 distance: 69 - 76: 8.158 distance: 71 - 72: 22.043 distance: 72 - 73: 16.637 distance: 73 - 74: 21.333 distance: 74 - 75: 22.961 distance: 76 - 77: 5.263 distance: 77 - 78: 4.368 distance: 77 - 80: 7.356 distance: 78 - 79: 5.952 distance: 80 - 81: 11.434 distance: 81 - 82: 16.418 distance: 81 - 83: 26.509