Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:20:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/12_2022/7ckz_30395_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/12_2022/7ckz_30395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/12_2022/7ckz_30395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/12_2022/7ckz_30395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/12_2022/7ckz_30395_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/12_2022/7ckz_30395_updated_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7222 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R GLU 132": "OE1" <-> "OE2" Residue "R ARG 227": "NH1" <-> "NH2" Residue "R GLU 232": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 8133 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1906 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2587 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2232 Unusual residues: {'CLR': 1, 'G4C': 1, 'LDP': 1} Classifications: {'peptide': 275, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 265, None: 3} Not linked: pdbres="LEU R 344 " pdbres="CLR R 501 " Not linked: pdbres="CLR R 501 " pdbres="LDP R 502 " Not linked: pdbres="LDP R 502 " pdbres="G4C R 503 " Chain breaks: 3 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 5.32, per 1000 atoms: 0.65 Number of scatterers: 8133 At special positions: 0 Unit cell: (96, 80, 125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 53 16.00 O 1492 8.00 N 1406 7.00 C 5180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.02 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " 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: 3.60 Conformation dependent library (CDL) restraints added in 1.3 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 11 sheets defined 37.4% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 15 through 39 removed outlier: 3.864A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 294 through 300 removed outlier: 4.357A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.756A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.769A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 23 through 49 Processing helix chain 'R' and resid 58 through 75 removed outlier: 4.464A pdb=" N PHE R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 Processing helix chain 'R' and resid 93 through 126 removed outlier: 3.603A pdb=" N CYS R 96 " --> pdb=" O GLY R 93 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASN R 97 " --> pdb=" O SER R 94 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR R 108 " --> pdb=" O MET R 105 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER R 126 " --> pdb=" O TRP R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 134 Processing helix chain 'R' and resid 137 through 160 removed outlier: 4.621A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 192 through 202 removed outlier: 3.849A pdb=" N SER R 197 " --> pdb=" O THR R 193 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL R 200 " --> pdb=" O ILE R 196 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE R 201 " --> pdb=" O SER R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 236 removed outlier: 4.324A pdb=" N ALA R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 277 removed outlier: 4.016A pdb=" N LYS R 269 " --> pdb=" O LYS R 265 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 292 Proline residue: R 287 - end of helix removed outlier: 3.882A pdb=" N LEU R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 330 removed outlier: 4.129A pdb=" N VAL R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE R 316 " --> pdb=" O THR R 312 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN R 323 " --> pdb=" O PHE R 319 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 335 through 343 removed outlier: 3.932A pdb=" N ALA R 340 " --> pdb=" O ASP R 336 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR R 343 " --> pdb=" O LYS R 339 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 3.505A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.581A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 4.039A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.563A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.774A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 222 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.364A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= H, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.830A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 121 through 125 removed outlier: 5.474A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.701A pdb=" N LEU N 20 " --> pdb=" O LEU N 81 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.503A pdb=" N GLY N 10 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 957 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: 2.42 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1304 1.31 - 1.44: 2324 1.44 - 1.57: 4601 1.57 - 1.70: 1 1.70 - 1.82: 74 Bond restraints: 8304 Sorted by residual: bond pdb=" C05 G4C R 503 " pdb=" N04 G4C R 503 " ideal model delta sigma weight residual 1.355 1.481 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C16 G4C R 503 " pdb=" C18 G4C R 503 " ideal model delta sigma weight residual 1.508 1.594 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" N ARG N 105 " pdb=" CA ARG N 105 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.80e+00 bond pdb=" N PHE B 234 " pdb=" CA PHE B 234 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.25e-02 6.40e+03 6.34e+00 bond pdb=" C08 G4C R 503 " pdb=" CL9 G4C R 503 " ideal model delta sigma weight residual 1.735 1.785 -0.050 2.00e-02 2.50e+03 6.18e+00 ... (remaining 8299 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.93: 186 106.93 - 113.71: 4632 113.71 - 120.48: 3253 120.48 - 127.26: 3110 127.26 - 134.04: 89 Bond angle restraints: 11270 Sorted by residual: angle pdb=" C03 G4C R 503 " pdb=" N04 G4C R 503 " pdb=" C05 G4C R 503 " ideal model delta sigma weight residual 118.75 128.13 -9.38 3.00e+00 1.11e-01 9.77e+00 angle pdb=" N ARG N 105 " pdb=" CA ARG N 105 " pdb=" C ARG N 105 " ideal model delta sigma weight residual 112.72 109.57 3.15 1.14e+00 7.69e-01 7.61e+00 angle pdb=" N VAL R 276 " pdb=" CA VAL R 276 " pdb=" C VAL R 276 " ideal model delta sigma weight residual 111.81 109.50 2.31 8.60e-01 1.35e+00 7.24e+00 angle pdb=" C06 G4C R 503 " pdb=" C05 G4C R 503 " pdb=" N04 G4C R 503 " ideal model delta sigma weight residual 116.82 124.06 -7.24 3.00e+00 1.11e-01 5.82e+00 angle pdb=" C03 G4C R 503 " pdb=" N04 G4C R 503 " pdb=" C16 G4C R 503 " ideal model delta sigma weight residual 119.52 112.47 7.05 3.00e+00 1.11e-01 5.53e+00 ... (remaining 11265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4466 17.94 - 35.88: 351 35.88 - 53.82: 75 53.82 - 71.76: 9 71.76 - 89.70: 8 Dihedral angle restraints: 4909 sinusoidal: 1887 harmonic: 3022 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -35.36 -50.64 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 186 " pdb=" CB CYS R 186 " ideal model delta sinusoidal sigma weight residual 93.00 58.75 34.25 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" CA ASP B 258 " pdb=" CB ASP B 258 " pdb=" CG ASP B 258 " pdb=" OD1 ASP B 258 " ideal model delta sinusoidal sigma weight residual -30.00 -87.95 57.95 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 4906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 796 0.031 - 0.062: 351 0.062 - 0.093: 94 0.093 - 0.124: 37 0.124 - 0.155: 4 Chirality restraints: 1282 Sorted by residual: chirality pdb=" C16 G4C R 503 " pdb=" C17 G4C R 503 " pdb=" C18 G4C R 503 " pdb=" N04 G4C R 503 " both_signs ideal model delta sigma weight residual False -2.47 -2.62 0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 1279 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 205 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO R 206 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO R 206 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 206 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO A 332 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO G 49 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.017 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 10 2.24 - 2.90: 3394 2.90 - 3.57: 12658 3.57 - 4.23: 21924 4.23 - 4.90: 35845 Nonbonded interactions: 73831 Sorted by model distance: nonbonded pdb=" OD1 ASN B 119 " pdb=" O GLY B 144 " model vdw 1.570 3.040 nonbonded pdb=" OD1 ASN B 119 " pdb=" C GLY B 144 " model vdw 1.910 3.270 nonbonded pdb=" OG SER R 202 " pdb=" O2 LDP R 502 " model vdw 2.070 2.440 nonbonded pdb=" O ILE R 154 " pdb=" OH TYR R 194 " model vdw 2.149 2.440 nonbonded pdb=" O ALA R 101 " pdb=" OG SER R 155 " model vdw 2.179 2.440 ... (remaining 73826 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 53 5.16 5 Cl 2 4.86 5 C 5180 2.51 5 N 1406 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 2.960 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.070 Process input model: 26.550 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 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 : 0.003 0.126 8304 Z= 0.206 Angle : 0.519 9.377 11270 Z= 0.296 Chirality : 0.039 0.155 1282 Planarity : 0.003 0.038 1422 Dihedral : 13.746 89.699 2933 Min Nonbonded Distance : 1.570 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.23), residues: 1017 helix: -1.83 (0.21), residues: 396 sheet: -2.71 (0.31), residues: 200 loop : -2.20 (0.28), residues: 421 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 270 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 274 average time/residue: 0.2426 time to fit residues: 85.3508 Evaluate side-chains 209 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 206 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0772 time to fit residues: 1.7853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.0470 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS N 13 GLN N 31 ASN N 39 GLN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 8304 Z= 0.272 Angle : 0.594 14.706 11270 Z= 0.306 Chirality : 0.043 0.277 1282 Planarity : 0.005 0.045 1422 Dihedral : 4.714 49.263 1140 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.25), residues: 1017 helix: -0.56 (0.25), residues: 397 sheet: -2.59 (0.33), residues: 195 loop : -1.67 (0.30), residues: 425 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 222 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 232 average time/residue: 0.2063 time to fit residues: 64.3811 Evaluate side-chains 203 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 192 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0770 time to fit residues: 2.8367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 90 optimal weight: 0.0040 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 29 GLN A 41 HIS A 236 GLN A 371 ASN A 377 ASN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS N 31 ASN R 60 ASN R 323 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 8304 Z= 0.240 Angle : 0.575 13.999 11270 Z= 0.291 Chirality : 0.042 0.302 1282 Planarity : 0.004 0.046 1422 Dihedral : 4.787 50.864 1140 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.26), residues: 1017 helix: -0.22 (0.25), residues: 389 sheet: -2.43 (0.34), residues: 197 loop : -1.42 (0.30), residues: 431 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 211 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 226 average time/residue: 0.1875 time to fit residues: 57.4874 Evaluate side-chains 205 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0663 time to fit residues: 3.2289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 0.0050 chunk 81 optimal weight: 0.1980 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 32 GLN B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 8304 Z= 0.284 Angle : 0.585 12.468 11270 Z= 0.295 Chirality : 0.043 0.274 1282 Planarity : 0.004 0.046 1422 Dihedral : 5.279 77.472 1140 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.26), residues: 1017 helix: -0.20 (0.25), residues: 397 sheet: -2.40 (0.34), residues: 207 loop : -1.30 (0.30), residues: 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 205 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 215 average time/residue: 0.2081 time to fit residues: 60.7245 Evaluate side-chains 205 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0837 time to fit residues: 4.0813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 8304 Z= 0.266 Angle : 0.585 12.039 11270 Z= 0.295 Chirality : 0.043 0.193 1282 Planarity : 0.004 0.049 1422 Dihedral : 5.406 80.757 1140 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.26), residues: 1017 helix: -0.08 (0.25), residues: 394 sheet: -2.37 (0.35), residues: 198 loop : -1.15 (0.30), residues: 425 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 209 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 219 average time/residue: 0.2198 time to fit residues: 64.5470 Evaluate side-chains 206 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 194 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0780 time to fit residues: 3.1233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 0.0870 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN A 377 ASN B 32 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN ** R 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 8304 Z= 0.234 Angle : 0.576 11.975 11270 Z= 0.291 Chirality : 0.042 0.205 1282 Planarity : 0.005 0.056 1422 Dihedral : 5.431 81.255 1140 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.26), residues: 1017 helix: -0.08 (0.25), residues: 406 sheet: -2.32 (0.35), residues: 198 loop : -1.10 (0.31), residues: 413 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 210 average time/residue: 0.2163 time to fit residues: 60.9845 Evaluate side-chains 199 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0825 time to fit residues: 2.9609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 371 ASN A 377 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 39 GLN R 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8304 Z= 0.208 Angle : 0.583 11.976 11270 Z= 0.291 Chirality : 0.043 0.211 1282 Planarity : 0.004 0.050 1422 Dihedral : 5.409 81.449 1140 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.26), residues: 1017 helix: 0.18 (0.25), residues: 397 sheet: -2.21 (0.35), residues: 198 loop : -1.09 (0.31), residues: 422 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 5 residues processed: 204 average time/residue: 0.2137 time to fit residues: 58.6644 Evaluate side-chains 190 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 185 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0798 time to fit residues: 1.9971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 88 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN ** R 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8304 Z= 0.222 Angle : 0.607 12.025 11270 Z= 0.302 Chirality : 0.043 0.212 1282 Planarity : 0.004 0.040 1422 Dihedral : 5.419 80.973 1140 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.26), residues: 1017 helix: 0.26 (0.25), residues: 400 sheet: -2.16 (0.36), residues: 199 loop : -1.07 (0.31), residues: 418 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 195 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 202 average time/residue: 0.1987 time to fit residues: 54.8551 Evaluate side-chains 192 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 186 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0885 time to fit residues: 2.2721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.0670 chunk 93 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN R 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 8304 Z= 0.266 Angle : 0.626 12.050 11270 Z= 0.311 Chirality : 0.044 0.214 1282 Planarity : 0.004 0.041 1422 Dihedral : 5.446 80.675 1140 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.26), residues: 1017 helix: 0.26 (0.26), residues: 400 sheet: -2.03 (0.37), residues: 183 loop : -1.03 (0.31), residues: 434 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 180 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 184 average time/residue: 0.2110 time to fit residues: 53.0018 Evaluate side-chains 180 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0966 time to fit residues: 1.7279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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: 55.3451 > 50: distance: 10 - 11: 14.674 distance: 11 - 12: 17.424 distance: 12 - 13: 18.424 distance: 12 - 14: 16.818 distance: 13 - 149: 22.192 distance: 14 - 15: 15.510 distance: 15 - 16: 10.027 distance: 15 - 18: 13.410 distance: 16 - 22: 13.272 distance: 19 - 20: 6.127 distance: 19 - 21: 10.614 distance: 22 - 23: 6.958 distance: 22 - 152: 4.755 distance: 23 - 24: 3.818 distance: 23 - 26: 10.973 distance: 24 - 25: 15.604 distance: 24 - 29: 11.648 distance: 26 - 27: 9.139 distance: 26 - 28: 15.314 distance: 29 - 30: 22.262 distance: 30 - 31: 12.299 distance: 30 - 33: 16.684 distance: 31 - 32: 8.087 distance: 31 - 38: 7.652 distance: 33 - 34: 6.165 distance: 34 - 35: 22.249 distance: 35 - 36: 4.151 distance: 35 - 37: 26.297 distance: 38 - 39: 7.551 distance: 38 - 44: 5.172 distance: 39 - 40: 21.030 distance: 39 - 42: 16.775 distance: 40 - 41: 19.488 distance: 40 - 45: 19.753 distance: 42 - 43: 7.585 distance: 43 - 44: 20.579 distance: 45 - 46: 22.622 distance: 46 - 47: 17.139 distance: 47 - 48: 25.968 distance: 47 - 49: 8.359 distance: 49 - 50: 23.658 distance: 50 - 51: 7.518 distance: 51 - 52: 23.825 distance: 51 - 53: 28.373 distance: 53 - 54: 6.384 distance: 54 - 55: 7.978 distance: 54 - 57: 15.138 distance: 55 - 56: 5.533 distance: 55 - 59: 22.113 distance: 57 - 58: 14.983 distance: 59 - 60: 4.931 distance: 59 - 111: 3.320 distance: 60 - 61: 6.472 distance: 60 - 63: 9.300 distance: 61 - 62: 10.383 distance: 61 - 67: 12.769 distance: 62 - 108: 10.638 distance: 63 - 64: 13.800 distance: 64 - 65: 12.472 distance: 64 - 66: 16.144 distance: 67 - 68: 8.035 distance: 68 - 69: 6.239 distance: 68 - 71: 3.372 distance: 69 - 70: 16.640 distance: 69 - 78: 6.272 distance: 71 - 72: 5.107 distance: 72 - 73: 3.901 distance: 73 - 74: 3.119 distance: 74 - 75: 3.278 distance: 75 - 77: 4.896