Starting phenix.real_space_refine (version: dev) on Tue Apr 5 09:12:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fih_31597/04_2022/7fih_31597_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fih_31597/04_2022/7fih_31597.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fih_31597/04_2022/7fih_31597_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fih_31597/04_2022/7fih_31597_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fih_31597/04_2022/7fih_31597_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fih_31597/04_2022/7fih_31597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fih_31597/04_2022/7fih_31597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fih_31597/04_2022/7fih_31597_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fih_31597/04_2022/7fih_31597_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "R ARG 53": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R ARG 112": "NH1" <-> "NH2" Residue "R GLU 115": "OE1" <-> "OE2" Residue "R ARG 124": "NH1" <-> "NH2" Residue "R ARG 136": "NH1" <-> "NH2" Residue "R GLU 148": "OE1" <-> "OE2" Residue "R GLU 187": "OE1" <-> "OE2" Residue "R GLU 206": "OE1" <-> "OE2" Residue "R GLU 211": "OE1" <-> "OE2" Residue "R ARG 219": "NH1" <-> "NH2" Residue "R ARG 247": "NH1" <-> "NH2" Residue "R GLU 263": "OE1" <-> "OE2" Residue "R ARG 342": "NH1" <-> "NH2" Residue "R GLU 346": "OE1" <-> "OE2" Residue "R ARG 395": "NH1" <-> "NH2" Residue "R GLU 520": "OE1" <-> "OE2" Residue "R TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 56": "OE1" <-> "OE2" Residue "Y ARG 6": "NH1" <-> "NH2" Residue "Y GLU 19": "OE1" <-> "OE2" Residue "Y ARG 94": "NH1" <-> "NH2" Residue "Y ARG 95": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 10853 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1972 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 4314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4314 Classifications: {'peptide': 550} Incomplete info: {'backbone_only': 9} Link IDs: {'PTRANS': 22, 'TRANS': 525, 'PCIS': 2} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "X" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 679 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain: "Y" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 97} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'55Z': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.33, per 1000 atoms: 0.58 Number of scatterers: 10853 At special positions: 0 Unit cell: (82.612, 97.83, 186.964, 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 91 16.00 O 2005 8.00 N 1872 7.00 C 6885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 156 " distance=2.05 Simple disulfide: pdb=" SG CYS R 279 " - pdb=" SG CYS R 343 " distance=2.03 Simple disulfide: pdb=" SG CYS R 280 " - pdb=" SG CYS R 353 " distance=2.03 Simple disulfide: pdb=" SG CYS R 439 " - pdb=" SG CYS R 514 " distance=2.03 Simple disulfide: pdb=" SG CYS X 7 " - pdb=" SG CYS X 31 " distance=2.03 Simple disulfide: pdb=" SG CYS X 10 " - pdb=" SG CYS X 60 " distance=2.03 Simple disulfide: pdb=" SG CYS X 28 " - pdb=" SG CYS X 82 " distance=2.03 Simple disulfide: pdb=" SG CYS X 32 " - pdb=" SG CYS X 84 " distance=2.03 Simple disulfide: pdb=" SG CYS X 59 " - pdb=" SG CYS X 87 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 9 " - pdb=" SG CYS Y 57 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 72 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 26 " - pdb=" SG CYS Y 110 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 34 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 38 " - pdb=" SG CYS Y 90 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 93 " - pdb=" SG CYS Y 100 " distance=2.04 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: 4.64 Conformation dependent library (CDL) restraints added in 1.6 seconds 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2604 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 16 sheets defined 28.9% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 14 through 37 Processing helix chain 'A' and resid 53 through 63 removed outlier: 4.367A pdb=" N TYR A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 322 through 339 removed outlier: 3.637A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 380 removed outlier: 3.600A pdb=" N GLN A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 242 through 244 No H-bonds generated for 'chain 'R' and resid 242 through 244' Processing helix chain 'R' and resid 262 through 264 No H-bonds generated for 'chain 'R' and resid 262 through 264' Processing helix chain 'R' and resid 276 through 282 Processing helix chain 'R' and resid 349 through 351 No H-bonds generated for 'chain 'R' and resid 349 through 351' Processing helix chain 'R' and resid 360 through 373 removed outlier: 4.064A pdb=" N VAL R 364 " --> pdb=" O ASP R 360 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TRP R 367 " --> pdb=" O ARG R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 375 through 385 Processing helix chain 'R' and resid 393 through 421 Processing helix chain 'R' and resid 426 through 434 removed outlier: 4.566A pdb=" N ILE R 431 " --> pdb=" O TYR R 427 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP R 432 " --> pdb=" O ASN R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 437 through 469 Processing helix chain 'R' and resid 480 through 497 Processing helix chain 'R' and resid 500 through 503 Processing helix chain 'R' and resid 522 through 553 Processing helix chain 'R' and resid 564 through 593 Proline residue: R 584 - end of helix Processing helix chain 'R' and resid 601 through 611 removed outlier: 3.634A pdb=" N LYS R 605 " --> pdb=" O VAL R 601 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL R 606 " --> pdb=" O THR R 602 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU R 607 " --> pdb=" O ASN R 603 " (cutoff:3.500A) Processing helix chain 'R' and resid 614 through 623 Proline residue: R 620 - end of helix Processing helix chain 'R' and resid 628 through 641 Processing helix chain 'X' and resid 41 through 44 No H-bonds generated for 'chain 'X' and resid 41 through 44' Processing sheet with id= A, first strand: chain 'A' and resid 218 through 223 removed outlier: 6.649A pdb=" N ALA A 243 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU A 46 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 245 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.678A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.246A 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: 3.869A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.488A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.669A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.174A 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: 6.758A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 306 through 308 removed outlier: 3.698A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.731A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 53 through 57 removed outlier: 6.627A pdb=" N LYS R 77 " --> pdb=" O LEU R 54 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU R 56 " --> pdb=" O LYS R 77 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLU R 79 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLU R 102 " --> pdb=" O ILE R 78 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE R 80 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU R 104 " --> pdb=" O ILE R 80 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR R 127 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE R 105 " --> pdb=" O TYR R 127 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N SER R 129 " --> pdb=" O ILE R 105 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE R 152 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE R 130 " --> pdb=" O ILE R 152 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU R 154 " --> pdb=" O ILE R 130 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU R 179 " --> pdb=" O THR R 200 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU R 202 " --> pdb=" O LEU R 179 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N THR R 226 " --> pdb=" O LEU R 202 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG R 247 " --> pdb=" O LEU R 227 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'X' and resid 11 through 14 Processing sheet with id= K, first strand: chain 'X' and resid 34 through 38 Processing sheet with id= L, first strand: chain 'X' and resid 65 through 69 Processing sheet with id= M, first strand: chain 'X' and resid 59 through 64 removed outlier: 6.641A pdb=" N ALA X 81 " --> pdb=" O LYS X 63 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'Y' and resid 10 through 18 Processing sheet with id= O, first strand: chain 'Y' and resid 62 through 68 Processing sheet with id= P, first strand: chain 'Y' and resid 56 through 61 removed outlier: 6.835A pdb=" N SER Y 87 " --> pdb=" O ARG Y 60 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 5.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1762 1.25 - 1.40: 2700 1.40 - 1.54: 6355 1.54 - 1.68: 136 1.68 - 1.83: 123 Bond restraints: 11076 Sorted by residual: bond pdb=" C10 55Z R 801 " pdb=" C9 55Z R 801 " ideal model delta sigma weight residual 1.617 1.383 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C33 55Z R 801 " pdb=" C34 55Z R 801 " ideal model delta sigma weight residual 1.527 1.300 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C15 55Z R 801 " pdb=" S16 55Z R 801 " ideal model delta sigma weight residual 1.580 1.789 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C30 55Z R 801 " pdb=" C31 55Z R 801 " ideal model delta sigma weight residual 1.527 1.319 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C8 55Z R 801 " pdb=" C9 55Z R 801 " ideal model delta sigma weight residual 1.438 1.271 0.167 2.00e-02 2.50e+03 6.96e+01 ... (remaining 11071 not shown) Histogram of bond angle deviations from ideal: 91.99 - 100.65: 8 100.65 - 109.30: 858 109.30 - 117.95: 7474 117.95 - 126.61: 6524 126.61 - 135.26: 151 Bond angle restraints: 15015 Sorted by residual: angle pdb=" N ARG A 255 " pdb=" CA ARG A 255 " pdb=" C ARG A 255 " ideal model delta sigma weight residual 112.38 98.44 13.94 1.22e+00 6.72e-01 1.31e+02 angle pdb=" CA ASP A 252 " pdb=" C ASP A 252 " pdb=" N TYR A 253 " ideal model delta sigma weight residual 115.89 103.49 12.40 1.40e+00 5.10e-01 7.85e+01 angle pdb=" C6 55Z R 801 " pdb=" C8 55Z R 801 " pdb=" C9 55Z R 801 " ideal model delta sigma weight residual 153.28 127.48 25.80 3.00e+00 1.11e-01 7.40e+01 angle pdb=" C6 55Z R 801 " pdb=" C8 55Z R 801 " pdb=" S16 55Z R 801 " ideal model delta sigma weight residual 94.60 120.14 -25.54 3.00e+00 1.11e-01 7.25e+01 angle pdb=" CA ASN A 254 " pdb=" C ASN A 254 " pdb=" O ASN A 254 " ideal model delta sigma weight residual 120.51 112.58 7.93 1.43e+00 4.89e-01 3.07e+01 ... (remaining 15010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.31: 6240 22.31 - 44.62: 402 44.62 - 66.93: 35 66.93 - 89.24: 18 89.24 - 111.55: 2 Dihedral angle restraints: 6697 sinusoidal: 2675 harmonic: 4022 Sorted by residual: dihedral pdb=" C ASN A 254 " pdb=" N ASN A 254 " pdb=" CA ASN A 254 " pdb=" CB ASN A 254 " ideal model delta harmonic sigma weight residual -122.60 -153.16 30.56 0 2.50e+00 1.60e-01 1.49e+02 dihedral pdb=" N ASN A 254 " pdb=" C ASN A 254 " pdb=" CA ASN A 254 " pdb=" CB ASN A 254 " ideal model delta harmonic sigma weight residual 122.80 152.93 -30.13 0 2.50e+00 1.60e-01 1.45e+02 dihedral pdb=" CB CYS X 10 " pdb=" SG CYS X 10 " pdb=" SG CYS X 60 " pdb=" CB CYS X 60 " ideal model delta sinusoidal sigma weight residual 93.00 168.78 -75.78 1 1.00e+01 1.00e-02 7.24e+01 ... (remaining 6694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.247: 1711 0.247 - 0.495: 2 0.495 - 0.742: 0 0.742 - 0.989: 0 0.989 - 1.236: 1 Chirality restraints: 1714 Sorted by residual: chirality pdb=" CA ASN A 254 " pdb=" N ASN A 254 " pdb=" C ASN A 254 " pdb=" CB ASN A 254 " both_signs ideal model delta sigma weight residual False 2.51 1.27 1.24 2.00e-01 2.50e+01 3.82e+01 chirality pdb=" CA ARG A 255 " pdb=" N ARG A 255 " pdb=" C ARG A 255 " pdb=" CB ARG A 255 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA CYS X 84 " pdb=" N CYS X 84 " pdb=" C CYS X 84 " pdb=" CB CYS X 84 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1711 not shown) Planarity restraints: 1917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 252 " -0.034 2.00e-02 2.50e+03 7.69e-02 5.91e+01 pdb=" C ASP A 252 " 0.133 2.00e-02 2.50e+03 pdb=" O ASP A 252 " -0.055 2.00e-02 2.50e+03 pdb=" N TYR A 253 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU R 354 " 0.018 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" CD GLU R 354 " -0.066 2.00e-02 2.50e+03 pdb=" OE1 GLU R 354 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU R 354 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 55Z R 801 " -0.005 2.00e-02 2.50e+03 1.78e-02 1.03e+01 pdb=" C11 55Z R 801 " -0.007 2.00e-02 2.50e+03 pdb=" C13 55Z R 801 " -0.015 2.00e-02 2.50e+03 pdb=" C15 55Z R 801 " -0.001 2.00e-02 2.50e+03 pdb=" C19 55Z R 801 " 0.021 2.00e-02 2.50e+03 pdb=" C6 55Z R 801 " 0.044 2.00e-02 2.50e+03 pdb=" C8 55Z R 801 " -0.025 2.00e-02 2.50e+03 pdb=" C9 55Z R 801 " -0.018 2.00e-02 2.50e+03 pdb=" N12 55Z R 801 " 0.004 2.00e-02 2.50e+03 pdb=" N14 55Z R 801 " -0.003 2.00e-02 2.50e+03 pdb=" N35 55Z R 801 " -0.013 2.00e-02 2.50e+03 pdb=" S16 55Z R 801 " -0.001 2.00e-02 2.50e+03 pdb=" S17 55Z R 801 " 0.017 2.00e-02 2.50e+03 ... (remaining 1914 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 115 2.55 - 3.14: 9033 3.14 - 3.72: 16641 3.72 - 4.31: 22461 4.31 - 4.90: 38566 Nonbonded interactions: 86816 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 1.962 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.079 2.440 nonbonded pdb=" O ASP R 518 " pdb=" OG SER R 524 " model vdw 2.114 2.440 nonbonded pdb=" OH TYR R 359 " pdb=" OD1 ASN R 603 " model vdw 2.128 2.440 nonbonded pdb=" ND2 ASN R 507 " pdb=" OD2 ASP R 518 " model vdw 2.160 2.520 ... (remaining 86811 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: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 6885 2.51 5 N 1872 2.21 5 O 2005 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=0.00 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 4.540 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 32.180 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.234 11076 Z= 0.368 Angle : 0.829 25.804 15015 Z= 0.449 Chirality : 0.052 1.236 1714 Planarity : 0.005 0.077 1917 Dihedral : 14.137 111.549 4048 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.30 % Favored : 96.63 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.51 % 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: -0.18 (0.24), residues: 1365 helix: 1.38 (0.27), residues: 385 sheet: -1.69 (0.28), residues: 301 loop : -0.11 (0.26), residues: 679 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 299 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 301 average time/residue: 0.2812 time to fit residues: 112.5352 Evaluate side-chains 246 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0834 time to fit residues: 1.6863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS R 158 ASN ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 476 GLN ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 615 ASN Y 58 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 11076 Z= 0.274 Angle : 0.676 9.283 15015 Z= 0.351 Chirality : 0.046 0.165 1714 Planarity : 0.006 0.092 1917 Dihedral : 5.753 79.802 1507 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.23), residues: 1365 helix: 1.85 (0.27), residues: 386 sheet: -1.61 (0.27), residues: 300 loop : -0.15 (0.25), residues: 679 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 301 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 308 average time/residue: 0.2593 time to fit residues: 109.3028 Evaluate side-chains 272 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 261 time to evaluate : 1.263 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1327 time to fit residues: 4.1589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 239 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** R 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 377 ASN ** R 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 476 GLN ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 615 ASN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 11076 Z= 0.262 Angle : 0.640 8.374 15015 Z= 0.335 Chirality : 0.046 0.185 1714 Planarity : 0.006 0.084 1917 Dihedral : 5.375 79.213 1507 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.03 (0.23), residues: 1365 helix: 1.91 (0.27), residues: 393 sheet: -1.47 (0.27), residues: 295 loop : -0.33 (0.24), residues: 677 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 280 time to evaluate : 1.423 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 15 residues processed: 294 average time/residue: 0.2615 time to fit residues: 104.3551 Evaluate side-chains 273 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 258 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1256 time to fit residues: 4.9365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 63 optimal weight: 0.0020 chunk 13 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 116 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN B 44 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 615 ASN R 619 ASN Y 54 GLN Y 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.120 11076 Z= 0.214 Angle : 0.645 11.680 15015 Z= 0.332 Chirality : 0.044 0.216 1714 Planarity : 0.005 0.080 1917 Dihedral : 5.209 75.354 1507 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.21 (0.23), residues: 1365 helix: 2.13 (0.27), residues: 389 sheet: -1.40 (0.28), residues: 294 loop : -0.24 (0.24), residues: 682 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 274 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 280 average time/residue: 0.2746 time to fit residues: 104.3877 Evaluate side-chains 264 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 253 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1367 time to fit residues: 4.3111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 111 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 ASN ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 615 ASN R 619 ASN X 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 11076 Z= 0.220 Angle : 0.646 12.888 15015 Z= 0.330 Chirality : 0.044 0.209 1714 Planarity : 0.005 0.084 1917 Dihedral : 5.148 74.450 1507 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.22 (0.23), residues: 1365 helix: 2.11 (0.27), residues: 390 sheet: -1.40 (0.29), residues: 299 loop : -0.19 (0.24), residues: 676 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 269 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 285 average time/residue: 0.2547 time to fit residues: 99.9021 Evaluate side-chains 273 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 260 time to evaluate : 1.288 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0993 time to fit residues: 4.2600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 5.9990 chunk 117 optimal weight: 0.0020 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 125 optimal weight: 0.0070 overall best weight: 0.5208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 155 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 619 ASN Y 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.157 11076 Z= 0.219 Angle : 0.652 12.896 15015 Z= 0.337 Chirality : 0.044 0.169 1714 Planarity : 0.005 0.088 1917 Dihedral : 5.081 72.269 1507 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.17 (0.23), residues: 1365 helix: 1.94 (0.27), residues: 399 sheet: -1.30 (0.29), residues: 296 loop : -0.25 (0.24), residues: 670 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 272 time to evaluate : 1.326 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 282 average time/residue: 0.2655 time to fit residues: 102.9172 Evaluate side-chains 267 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 257 time to evaluate : 1.283 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1316 time to fit residues: 5.8482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 81 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 80 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.790 11076 Z= 0.513 Angle : 1.162 106.001 15015 Z= 0.493 Chirality : 0.044 0.330 1714 Planarity : 0.005 0.101 1917 Dihedral : 5.137 72.263 1507 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.08 % 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: 0.14 (0.23), residues: 1365 helix: 1.93 (0.27), residues: 399 sheet: -1.30 (0.29), residues: 296 loop : -0.28 (0.24), residues: 670 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 259 time to evaluate : 1.325 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 261 average time/residue: 0.2576 time to fit residues: 91.7340 Evaluate side-chains 249 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 1.246 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1268 time to fit residues: 1.9809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.777 11076 Z= 0.515 Angle : 1.161 106.100 15015 Z= 0.492 Chirality : 0.044 0.331 1714 Planarity : 0.005 0.100 1917 Dihedral : 5.137 72.267 1507 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.08 % 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: 0.14 (0.23), residues: 1365 helix: 1.92 (0.27), residues: 399 sheet: -1.30 (0.29), residues: 296 loop : -0.27 (0.24), residues: 670 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 1.437 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 248 average time/residue: 0.2607 time to fit residues: 88.1181 Evaluate side-chains 252 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 1.382 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1076 time to fit residues: 2.1604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 124 optimal weight: 50.0000 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.777 11076 Z= 0.515 Angle : 1.161 106.100 15015 Z= 0.492 Chirality : 0.044 0.331 1714 Planarity : 0.005 0.100 1917 Dihedral : 5.137 72.267 1507 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.08 % 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: 0.14 (0.23), residues: 1365 helix: 1.92 (0.27), residues: 399 sheet: -1.30 (0.29), residues: 296 loop : -0.27 (0.24), residues: 670 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.350 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2762 time to fit residues: 93.7024 Evaluate side-chains 248 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.493 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 107 optimal weight: 0.0370 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 0.0870 chunk 65 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.777 11076 Z= 0.515 Angle : 1.161 106.100 15015 Z= 0.492 Chirality : 0.044 0.331 1714 Planarity : 0.005 0.100 1917 Dihedral : 5.137 72.267 1507 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.08 % 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: 0.14 (0.23), residues: 1365 helix: 1.92 (0.27), residues: 399 sheet: -1.30 (0.29), residues: 296 loop : -0.27 (0.24), residues: 670 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.331 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2745 time to fit residues: 93.2408 Evaluate side-chains 250 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.335 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.130266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.118099 restraints weight = 20980.827| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.51 r_work: 0.3713 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 2.29 restraints_weight: 0.2500 r_work: 0.3697 rms_B_bonded: 2.31 restraints_weight: 0.1250 r_work: 0.3688 rms_B_bonded: 2.37 restraints_weight: 0.0625 r_work: 0.3678 rms_B_bonded: 2.47 restraints_weight: 0.0312 r_work: 0.3668 rms_B_bonded: 2.58 restraints_weight: 0.0156 r_work: 0.3658 rms_B_bonded: 2.73 restraints_weight: 0.0078 r_work: 0.3647 rms_B_bonded: 2.90 restraints_weight: 0.0039 r_work: 0.3635 rms_B_bonded: 3.09 restraints_weight: 0.0020 r_work: 0.3622 rms_B_bonded: 3.32 restraints_weight: 0.0010 r_work: 0.3608 rms_B_bonded: 3.57 restraints_weight: 0.0005 r_work: 0.3594 rms_B_bonded: 3.86 restraints_weight: 0.0002 r_work: 0.3578 rms_B_bonded: 4.19 restraints_weight: 0.0001 r_work: 0.3561 rms_B_bonded: 4.55 restraints_weight: 0.0001 r_work: 0.3543 rms_B_bonded: 4.96 restraints_weight: 0.0000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.777 11076 Z= 0.515 Angle : 1.161 106.100 15015 Z= 0.492 Chirality : 0.044 0.331 1714 Planarity : 0.005 0.100 1917 Dihedral : 5.137 72.267 1507 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.08 % 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: 0.14 (0.23), residues: 1365 helix: 1.92 (0.27), residues: 399 sheet: -1.30 (0.29), residues: 296 loop : -0.27 (0.24), residues: 670 =============================================================================== Job complete usr+sys time: 2696.61 seconds wall clock time: 49 minutes 44.10 seconds (2984.10 seconds total)