Starting phenix.real_space_refine on Thu Feb 15 13:02:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fih_31597/02_2024/7fih_31597_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fih_31597/02_2024/7fih_31597.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fih_31597/02_2024/7fih_31597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fih_31597/02_2024/7fih_31597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fih_31597/02_2024/7fih_31597_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fih_31597/02_2024/7fih_31597_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.040 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 1455 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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. 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-5238/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: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 525} 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: 6.14, per 1000 atoms: 0.57 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: 4.31 Conformation dependent library (CDL) restraints added in 2.0 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: 2.32 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: 3.19 Time building geometry restraints manager: 4.67 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=" C33 55Z R 801 " pdb=" C34 55Z R 801 " ideal model delta sigma weight residual 1.517 1.300 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C30 55Z R 801 " pdb=" C31 55Z R 801 " ideal model delta sigma weight residual 1.516 1.319 0.197 2.00e-02 2.50e+03 9.67e+01 bond pdb=" C6 55Z R 801 " pdb=" O7 55Z R 801 " ideal model delta sigma weight residual 1.234 1.110 0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C8 55Z R 801 " pdb=" C9 55Z R 801 " ideal model delta sigma weight residual 1.382 1.271 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C34 55Z R 801 " pdb=" N29 55Z R 801 " ideal model delta sigma weight residual 1.458 1.349 0.109 2.00e-02 2.50e+03 2.95e+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=" C13 55Z R 801 " pdb=" S17 55Z R 801 " pdb=" C18 55Z R 801 " ideal model delta sigma weight residual 102.86 119.70 -16.84 3.00e+00 1.11e-01 3.15e+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 angle pdb=" O ASP A 252 " pdb=" C ASP A 252 " pdb=" N TYR A 253 " ideal model delta sigma weight residual 122.43 128.93 -6.50 1.30e+00 5.92e-01 2.50e+01 ... (remaining 15010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 6057 17.62 - 35.24: 530 35.24 - 52.85: 94 52.85 - 70.47: 18 70.47 - 88.09: 15 Dihedral angle restraints: 6714 sinusoidal: 2692 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 6711 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 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: 1.000 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: 4.070 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.850 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.217 11076 Z= 0.344 Angle : 0.760 16.837 15015 Z= 0.435 Chirality : 0.052 1.236 1714 Planarity : 0.005 0.077 1917 Dihedral : 13.977 88.091 4065 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 % Allowed : 0.33 % Favored : 99.50 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.005 0.001 HIS B 54 PHE 0.013 0.001 PHE B 234 TYR 0.032 0.001 TYR R 389 ARG 0.017 0.001 ARG A 346 *********************** 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 : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7711 (t0) cc_final: 0.7453 (t0) REVERT: A 273 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7797 (ttm-80) REVERT: B 127 LYS cc_start: 0.7346 (mttp) cc_final: 0.6987 (mttp) REVERT: B 315 VAL cc_start: 0.8258 (t) cc_final: 0.8006 (p) REVERT: R 228 ASP cc_start: 0.7393 (t0) cc_final: 0.7172 (t0) REVERT: X 29 MET cc_start: 0.4549 (mtm) cc_final: 0.4333 (mtm) REVERT: X 46 THR cc_start: 0.7606 (m) cc_final: 0.7379 (t) REVERT: Y 7 PRO cc_start: 0.6142 (Cg_endo) cc_final: 0.5907 (Cg_exo) outliers start: 2 outliers final: 1 residues processed: 301 average time/residue: 0.2880 time to fit residues: 114.2276 Evaluate side-chains 249 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASN 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: 6.9990 chunk 54 optimal weight: 0.7980 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: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 254 ASN ** 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: 0.7035 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11076 Z= 0.225 Angle : 0.640 8.515 15015 Z= 0.330 Chirality : 0.045 0.163 1714 Planarity : 0.004 0.064 1917 Dihedral : 5.513 58.346 1526 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.09 % Allowed : 10.28 % Favored : 87.64 % 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: 0.14 (0.23), residues: 1365 helix: 1.89 (0.27), residues: 387 sheet: -1.55 (0.27), residues: 300 loop : -0.07 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS A 377 PHE 0.013 0.001 PHE B 199 TYR 0.027 0.002 TYR R 389 ARG 0.007 0.001 ARG B 219 *********************** 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 329 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 304 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7457 (tp30) cc_final: 0.7012 (tp30) REVERT: A 262 ASP cc_start: 0.7747 (t0) cc_final: 0.7299 (t0) REVERT: A 265 SER cc_start: 0.8772 (t) cc_final: 0.8567 (t) REVERT: A 333 ASP cc_start: 0.7653 (t0) cc_final: 0.7419 (t0) REVERT: B 51 LEU cc_start: 0.8819 (mp) cc_final: 0.8595 (mp) REVERT: B 155 ASN cc_start: 0.8120 (t0) cc_final: 0.7237 (t0) REVERT: B 163 ASP cc_start: 0.7789 (t70) cc_final: 0.7378 (t0) REVERT: B 200 VAL cc_start: 0.8979 (m) cc_final: 0.8689 (p) REVERT: B 259 GLN cc_start: 0.7573 (pt0) cc_final: 0.7358 (pt0) REVERT: B 315 VAL cc_start: 0.7922 (t) cc_final: 0.7697 (p) REVERT: R 81 SER cc_start: 0.8518 (p) cc_final: 0.8126 (t) REVERT: R 108 THR cc_start: 0.8011 (m) cc_final: 0.7261 (p) REVERT: R 253 SER cc_start: 0.7635 (t) cc_final: 0.7334 (t) REVERT: R 389 TYR cc_start: 0.7268 (m-80) cc_final: 0.6958 (m-80) REVERT: R 553 VAL cc_start: 0.8549 (t) cc_final: 0.8276 (p) REVERT: R 559 MET cc_start: 0.5261 (tpt) cc_final: 0.4671 (tpt) REVERT: R 571 MET cc_start: 0.7261 (mtp) cc_final: 0.7040 (mtp) outliers start: 25 outliers final: 11 residues processed: 315 average time/residue: 0.2532 time to fit residues: 108.5133 Evaluate side-chains 275 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 264 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 388 ARG Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain R residue 628 LYS Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Y residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS R 150 ASN ** R 370 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 46 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11076 Z= 0.239 Angle : 0.611 6.863 15015 Z= 0.319 Chirality : 0.045 0.184 1714 Planarity : 0.005 0.067 1917 Dihedral : 5.234 41.719 1524 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.76 % Allowed : 15.20 % Favored : 82.04 % 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: 0.22 (0.23), residues: 1365 helix: 2.11 (0.27), residues: 386 sheet: -1.42 (0.28), residues: 304 loop : -0.15 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.009 0.001 HIS A 347 PHE 0.021 0.001 PHE R 587 TYR 0.020 0.001 TYR R 389 ARG 0.007 0.001 ARG A 273 *********************** 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 317 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 284 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7513 (tp30) cc_final: 0.7073 (tp30) REVERT: A 233 LYS cc_start: 0.7425 (ttmm) cc_final: 0.7127 (tppp) REVERT: A 262 ASP cc_start: 0.7629 (t0) cc_final: 0.7361 (t0) REVERT: A 267 TRP cc_start: 0.8640 (t-100) cc_final: 0.8387 (t-100) REVERT: A 358 ASP cc_start: 0.6609 (t0) cc_final: 0.6343 (t0) REVERT: B 51 LEU cc_start: 0.8862 (mp) cc_final: 0.8648 (mp) REVERT: B 163 ASP cc_start: 0.7882 (t70) cc_final: 0.7408 (t0) REVERT: B 189 SER cc_start: 0.7976 (p) cc_final: 0.7504 (t) REVERT: B 214 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7707 (mtt90) REVERT: B 259 GLN cc_start: 0.7705 (pt0) cc_final: 0.7484 (pt0) REVERT: G 16 VAL cc_start: 0.7658 (t) cc_final: 0.7428 (p) REVERT: R 81 SER cc_start: 0.8511 (p) cc_final: 0.8179 (t) REVERT: R 108 THR cc_start: 0.8209 (m) cc_final: 0.7530 (p) REVERT: R 253 SER cc_start: 0.8251 (t) cc_final: 0.7929 (t) REVERT: Y 92 LEU cc_start: 0.8991 (mt) cc_final: 0.8781 (mm) outliers start: 33 outliers final: 18 residues processed: 300 average time/residue: 0.2551 time to fit residues: 104.7121 Evaluate side-chains 273 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 255 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 522 THR Chi-restraints excluded: chain X residue 46 THR Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Y residue 26 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 chunk 35 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 ASN ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 615 ASN Y 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11076 Z= 0.195 Angle : 0.589 7.934 15015 Z= 0.304 Chirality : 0.043 0.167 1714 Planarity : 0.004 0.067 1917 Dihedral : 5.064 40.559 1524 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.01 % Allowed : 17.29 % Favored : 79.70 % 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: 0.27 (0.23), residues: 1365 helix: 2.17 (0.27), residues: 389 sheet: -1.30 (0.29), residues: 300 loop : -0.20 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.025 0.001 PHE R 493 TYR 0.021 0.001 TYR R 389 ARG 0.009 0.001 ARG A 273 *********************** 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 308 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 272 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.6975 (ttm) cc_final: 0.6531 (mtt) REVERT: A 27 GLU cc_start: 0.7470 (tp30) cc_final: 0.7041 (tp30) REVERT: A 262 ASP cc_start: 0.7551 (t0) cc_final: 0.7324 (t0) REVERT: A 267 TRP cc_start: 0.8687 (t-100) cc_final: 0.7844 (t-100) REVERT: A 317 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6228 (tm-30) REVERT: A 358 ASP cc_start: 0.6675 (t0) cc_final: 0.6435 (t0) REVERT: B 51 LEU cc_start: 0.8815 (mp) cc_final: 0.8609 (mp) REVERT: B 155 ASN cc_start: 0.8160 (t0) cc_final: 0.7898 (t0) REVERT: B 163 ASP cc_start: 0.7695 (t70) cc_final: 0.7246 (t0) REVERT: B 189 SER cc_start: 0.7872 (p) cc_final: 0.7376 (t) REVERT: B 259 GLN cc_start: 0.7607 (pt0) cc_final: 0.7378 (pt0) REVERT: B 293 ASN cc_start: 0.8598 (p0) cc_final: 0.8285 (p0) REVERT: R 81 SER cc_start: 0.8366 (p) cc_final: 0.8091 (t) REVERT: R 108 THR cc_start: 0.8138 (m) cc_final: 0.7456 (p) REVERT: R 121 ASN cc_start: 0.6849 (t0) cc_final: 0.6470 (m-40) REVERT: R 253 SER cc_start: 0.8437 (t) cc_final: 0.8138 (t) REVERT: R 262 ARG cc_start: 0.7122 (tpt90) cc_final: 0.6733 (tpt90) REVERT: R 398 MET cc_start: 0.7361 (tpp) cc_final: 0.7134 (tpp) REVERT: R 484 ILE cc_start: 0.8584 (mm) cc_final: 0.8138 (tp) REVERT: R 559 MET cc_start: 0.5360 (tpt) cc_final: 0.5000 (tpt) REVERT: X 76 VAL cc_start: 0.6731 (t) cc_final: 0.6360 (p) outliers start: 36 outliers final: 19 residues processed: 288 average time/residue: 0.2578 time to fit residues: 100.7374 Evaluate side-chains 279 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 260 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 388 ARG Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 543 CYS Chi-restraints excluded: chain X residue 29 MET Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Y residue 26 CYS Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 76 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 GLN Y 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11076 Z= 0.210 Angle : 0.589 7.947 15015 Z= 0.304 Chirality : 0.044 0.160 1714 Planarity : 0.004 0.068 1917 Dihedral : 5.039 38.536 1524 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.84 % Allowed : 18.63 % Favored : 78.53 % 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: 0.32 (0.23), residues: 1365 helix: 2.21 (0.27), residues: 389 sheet: -1.24 (0.28), residues: 307 loop : -0.17 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.026 0.001 PHE R 493 TYR 0.015 0.001 TYR R 389 ARG 0.006 0.001 ARG B 42 *********************** 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 310 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 276 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.6972 (ttm) cc_final: 0.6551 (mtt) REVERT: A 27 GLU cc_start: 0.7575 (tp30) cc_final: 0.7002 (tp30) REVERT: A 262 ASP cc_start: 0.7572 (t0) cc_final: 0.7343 (t0) REVERT: A 265 SER cc_start: 0.8881 (t) cc_final: 0.8678 (t) REVERT: A 267 TRP cc_start: 0.8712 (t-100) cc_final: 0.8408 (t-100) REVERT: A 358 ASP cc_start: 0.6658 (t0) cc_final: 0.6403 (t0) REVERT: B 51 LEU cc_start: 0.8844 (mp) cc_final: 0.8625 (mp) REVERT: B 163 ASP cc_start: 0.7831 (t70) cc_final: 0.7221 (t0) REVERT: B 189 SER cc_start: 0.7829 (p) cc_final: 0.7373 (t) REVERT: B 259 GLN cc_start: 0.7668 (pt0) cc_final: 0.7423 (pt0) REVERT: B 293 ASN cc_start: 0.8599 (p0) cc_final: 0.8066 (p0) REVERT: R 81 SER cc_start: 0.8334 (p) cc_final: 0.8104 (t) REVERT: R 108 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7475 (p) REVERT: R 121 ASN cc_start: 0.6873 (t0) cc_final: 0.6438 (m-40) REVERT: R 143 LYS cc_start: 0.4243 (pttt) cc_final: 0.3889 (pttm) REVERT: R 253 SER cc_start: 0.8547 (t) cc_final: 0.8239 (t) REVERT: R 262 ARG cc_start: 0.7168 (tpt90) cc_final: 0.6810 (tpt90) REVERT: R 279 CYS cc_start: 0.6126 (m) cc_final: 0.5757 (m) REVERT: R 398 MET cc_start: 0.7380 (tpp) cc_final: 0.7153 (tpp) REVERT: R 484 ILE cc_start: 0.8566 (mm) cc_final: 0.8129 (tp) REVERT: R 559 MET cc_start: 0.5692 (tpt) cc_final: 0.5309 (tpt) outliers start: 34 outliers final: 25 residues processed: 290 average time/residue: 0.2602 time to fit residues: 102.7454 Evaluate side-chains 289 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 263 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 351 ASN Chi-restraints excluded: chain R residue 388 ARG Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 522 THR Chi-restraints excluded: chain R residue 543 CYS Chi-restraints excluded: chain R residue 585 ILE Chi-restraints excluded: chain X residue 29 MET Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Y residue 26 CYS Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 92 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 0.0000 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 chunk 130 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 60 optimal weight: 0.0040 chunk 10 optimal weight: 0.0970 chunk 68 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 overall best weight: 0.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 615 ASN Y 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11076 Z= 0.161 Angle : 0.588 8.383 15015 Z= 0.299 Chirality : 0.042 0.158 1714 Planarity : 0.004 0.068 1917 Dihedral : 4.854 38.629 1524 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.59 % Allowed : 20.55 % Favored : 76.86 % 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: 0.41 (0.23), residues: 1365 helix: 2.32 (0.27), residues: 389 sheet: -1.14 (0.29), residues: 306 loop : -0.18 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.003 0.000 HIS B 183 PHE 0.026 0.001 PHE R 493 TYR 0.015 0.001 TYR R 389 ARG 0.008 0.001 ARG A 379 *********************** 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 303 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 272 time to evaluate : 1.282 Fit side-chains REVERT: A 25 MET cc_start: 0.6967 (ttm) cc_final: 0.6580 (mtt) REVERT: A 27 GLU cc_start: 0.7586 (tp30) cc_final: 0.7007 (tp30) REVERT: A 262 ASP cc_start: 0.7485 (t0) cc_final: 0.7256 (t0) REVERT: A 270 ARG cc_start: 0.7731 (ttp80) cc_final: 0.7424 (ttp80) REVERT: A 358 ASP cc_start: 0.6652 (t0) cc_final: 0.6398 (t0) REVERT: B 51 LEU cc_start: 0.8794 (mp) cc_final: 0.8593 (mp) REVERT: B 163 ASP cc_start: 0.7634 (t70) cc_final: 0.7217 (t0) REVERT: B 189 SER cc_start: 0.7843 (p) cc_final: 0.7388 (t) REVERT: B 259 GLN cc_start: 0.7507 (pt0) cc_final: 0.7285 (pt0) REVERT: B 293 ASN cc_start: 0.8485 (p0) cc_final: 0.8271 (p0) REVERT: R 81 SER cc_start: 0.8310 (p) cc_final: 0.8085 (t) REVERT: R 108 THR cc_start: 0.7886 (OUTLIER) cc_final: 0.7301 (p) REVERT: R 253 SER cc_start: 0.8488 (t) cc_final: 0.8183 (t) REVERT: R 262 ARG cc_start: 0.7124 (tpt90) cc_final: 0.6633 (tpt90) REVERT: R 419 ASP cc_start: 0.7936 (t0) cc_final: 0.7619 (t0) REVERT: R 484 ILE cc_start: 0.8547 (mm) cc_final: 0.8107 (tp) REVERT: Y 72 CYS cc_start: -0.1086 (OUTLIER) cc_final: -0.1338 (p) outliers start: 31 outliers final: 17 residues processed: 288 average time/residue: 0.2487 time to fit residues: 98.9403 Evaluate side-chains 270 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 251 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 351 ASN Chi-restraints excluded: chain R residue 388 ARG Chi-restraints excluded: chain R residue 474 LEU Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 26 CYS Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 92 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.0170 chunk 74 optimal weight: 4.9990 chunk 95 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 ASN ** R 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 619 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11076 Z= 0.202 Angle : 0.605 7.332 15015 Z= 0.310 Chirality : 0.043 0.167 1714 Planarity : 0.005 0.068 1917 Dihedral : 4.890 36.264 1524 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.68 % Allowed : 20.13 % Favored : 76.19 % 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: 0.43 (0.23), residues: 1365 helix: 2.33 (0.27), residues: 389 sheet: -1.15 (0.29), residues: 307 loop : -0.14 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.003 0.001 HIS R 429 PHE 0.026 0.001 PHE R 493 TYR 0.016 0.001 TYR A 308 ARG 0.011 0.001 ARG A 346 *********************** 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 325 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 281 time to evaluate : 1.407 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.6978 (ttm) cc_final: 0.6629 (mtt) REVERT: A 27 GLU cc_start: 0.7666 (tp30) cc_final: 0.7068 (tp30) REVERT: A 262 ASP cc_start: 0.7508 (t0) cc_final: 0.7139 (t0) REVERT: A 265 SER cc_start: 0.8877 (t) cc_final: 0.8668 (t) REVERT: A 358 ASP cc_start: 0.6676 (t0) cc_final: 0.6447 (t0) REVERT: B 51 LEU cc_start: 0.8797 (mp) cc_final: 0.8574 (mp) REVERT: B 86 THR cc_start: 0.8244 (p) cc_final: 0.7980 (p) REVERT: B 130 GLU cc_start: 0.6731 (mp0) cc_final: 0.6401 (mt-10) REVERT: B 155 ASN cc_start: 0.8127 (t0) cc_final: 0.7807 (t0) REVERT: B 163 ASP cc_start: 0.7774 (t70) cc_final: 0.7184 (t0) REVERT: B 189 SER cc_start: 0.7910 (p) cc_final: 0.7383 (t) REVERT: B 259 GLN cc_start: 0.7714 (pt0) cc_final: 0.7458 (pt0) REVERT: B 293 ASN cc_start: 0.8415 (p0) cc_final: 0.8180 (p0) REVERT: G 20 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8504 (mmmm) REVERT: G 58 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7200 (mp0) REVERT: R 108 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7352 (p) REVERT: R 253 SER cc_start: 0.8625 (t) cc_final: 0.8331 (t) REVERT: R 262 ARG cc_start: 0.7147 (tpt90) cc_final: 0.6771 (tpt90) REVERT: R 484 ILE cc_start: 0.8588 (mm) cc_final: 0.8144 (tp) REVERT: Y 72 CYS cc_start: -0.0809 (OUTLIER) cc_final: -0.1145 (p) outliers start: 44 outliers final: 33 residues processed: 305 average time/residue: 0.2568 time to fit residues: 106.5962 Evaluate side-chains 297 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 262 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 351 ASN Chi-restraints excluded: chain R residue 355 ASP Chi-restraints excluded: chain R residue 388 ARG Chi-restraints excluded: chain R residue 402 SER Chi-restraints excluded: chain R residue 474 LEU Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 522 THR Chi-restraints excluded: chain R residue 543 CYS Chi-restraints excluded: chain R residue 585 ILE Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Y residue 34 CYS Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 90 CYS Chi-restraints excluded: chain Y residue 92 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11076 Z= 0.347 Angle : 0.690 7.388 15015 Z= 0.358 Chirality : 0.047 0.180 1714 Planarity : 0.005 0.067 1917 Dihedral : 5.566 34.260 1524 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.43 % Allowed : 20.63 % Favored : 75.94 % 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: 2.01 (0.27), residues: 396 sheet: -1.42 (0.29), residues: 294 loop : -0.43 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.006 0.001 HIS R 192 PHE 0.027 0.002 PHE R 493 TYR 0.020 0.002 TYR A 308 ARG 0.007 0.001 ARG B 42 *********************** 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 334 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 293 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.7102 (ttm) cc_final: 0.6764 (mtt) REVERT: A 230 GLU cc_start: 0.7855 (tp30) cc_final: 0.7566 (tp30) REVERT: A 265 SER cc_start: 0.8944 (t) cc_final: 0.8702 (t) REVERT: A 360 GLU cc_start: 0.7814 (mp0) cc_final: 0.7379 (mp0) REVERT: B 33 ILE cc_start: 0.6515 (tt) cc_final: 0.6295 (tp) REVERT: B 51 LEU cc_start: 0.8888 (mp) cc_final: 0.8635 (mp) REVERT: B 155 ASN cc_start: 0.8287 (t0) cc_final: 0.7901 (t0) REVERT: B 189 SER cc_start: 0.7939 (p) cc_final: 0.7563 (t) REVERT: B 259 GLN cc_start: 0.7802 (pt0) cc_final: 0.7522 (pt0) REVERT: B 293 ASN cc_start: 0.8527 (p0) cc_final: 0.8255 (p0) REVERT: G 20 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8574 (mmmm) REVERT: G 58 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7434 (mp0) REVERT: R 108 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7537 (p) REVERT: R 143 LYS cc_start: 0.4882 (pttt) cc_final: 0.4444 (pttm) REVERT: R 253 SER cc_start: 0.8844 (t) cc_final: 0.8267 (p) REVERT: R 262 ARG cc_start: 0.7139 (tpt90) cc_final: 0.6721 (tpt90) REVERT: R 405 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7572 (t0) REVERT: R 419 ASP cc_start: 0.7991 (t0) cc_final: 0.7704 (t0) REVERT: X 84 CYS cc_start: 0.4900 (OUTLIER) cc_final: 0.4639 (m) outliers start: 41 outliers final: 30 residues processed: 310 average time/residue: 0.2557 time to fit residues: 107.7089 Evaluate side-chains 302 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 269 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 351 ASN Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 487 MET Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 522 THR Chi-restraints excluded: chain R residue 543 CYS Chi-restraints excluded: chain R residue 573 ILE Chi-restraints excluded: chain R residue 585 ILE Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 34 CYS Chi-restraints excluded: chain Y residue 42 THR Chi-restraints excluded: chain Y residue 44 VAL Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 90 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.0570 chunk 121 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 227 GLN B 44 GLN B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 619 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11076 Z= 0.219 Angle : 0.666 13.708 15015 Z= 0.338 Chirality : 0.045 0.212 1714 Planarity : 0.005 0.068 1917 Dihedral : 5.322 41.388 1524 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.92 % Allowed : 21.55 % Favored : 75.52 % 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: 0.23 (0.23), residues: 1365 helix: 2.23 (0.27), residues: 389 sheet: -1.37 (0.29), residues: 296 loop : -0.28 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 169 HIS 0.004 0.001 HIS R 192 PHE 0.025 0.001 PHE R 493 TYR 0.021 0.001 TYR R 612 ARG 0.010 0.001 ARG A 346 *********************** 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 296 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 261 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.7108 (ttm) cc_final: 0.6821 (mtt) REVERT: A 229 ASP cc_start: 0.7694 (p0) cc_final: 0.7474 (p0) REVERT: A 267 TRP cc_start: 0.8800 (t-100) cc_final: 0.8468 (t-100) REVERT: A 360 GLU cc_start: 0.7721 (mp0) cc_final: 0.7404 (mp0) REVERT: B 33 ILE cc_start: 0.6587 (tt) cc_final: 0.6302 (tp) REVERT: B 51 LEU cc_start: 0.8820 (mp) cc_final: 0.8550 (mp) REVERT: B 54 HIS cc_start: 0.7964 (OUTLIER) cc_final: 0.7319 (t70) REVERT: B 155 ASN cc_start: 0.8244 (t0) cc_final: 0.7887 (t0) REVERT: B 189 SER cc_start: 0.7927 (p) cc_final: 0.7526 (t) REVERT: B 214 ARG cc_start: 0.7783 (mtt90) cc_final: 0.7580 (mtt90) REVERT: B 259 GLN cc_start: 0.7698 (pt0) cc_final: 0.7432 (pt0) REVERT: B 293 ASN cc_start: 0.8445 (p0) cc_final: 0.8177 (p0) REVERT: G 25 ILE cc_start: 0.8606 (tp) cc_final: 0.8315 (pt) REVERT: G 58 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7498 (mp0) REVERT: R 108 THR cc_start: 0.7948 (OUTLIER) cc_final: 0.7317 (p) REVERT: R 143 LYS cc_start: 0.4262 (pttt) cc_final: 0.3771 (pttm) REVERT: R 253 SER cc_start: 0.8804 (t) cc_final: 0.8209 (p) REVERT: R 262 ARG cc_start: 0.7144 (tpt90) cc_final: 0.6755 (tpt90) REVERT: R 405 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7630 (t0) REVERT: R 484 ILE cc_start: 0.8568 (mm) cc_final: 0.8158 (tp) REVERT: X 84 CYS cc_start: 0.4703 (OUTLIER) cc_final: 0.4485 (m) REVERT: Y 43 ARG cc_start: 0.8479 (tpp80) cc_final: 0.8237 (tpp80) outliers start: 35 outliers final: 24 residues processed: 279 average time/residue: 0.2582 time to fit residues: 98.3108 Evaluate side-chains 285 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 257 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 351 ASN Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 522 THR Chi-restraints excluded: chain R residue 543 CYS Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Y residue 34 CYS Chi-restraints excluded: chain Y residue 42 THR Chi-restraints excluded: chain Y residue 44 VAL Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 90 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 44 GLN B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 476 GLN ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11076 Z= 0.217 Angle : 0.667 12.704 15015 Z= 0.338 Chirality : 0.045 0.188 1714 Planarity : 0.004 0.069 1917 Dihedral : 5.263 37.586 1524 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.51 % Allowed : 22.47 % Favored : 75.02 % 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: 0.24 (0.24), residues: 1365 helix: 2.23 (0.27), residues: 389 sheet: -1.36 (0.29), residues: 296 loop : -0.28 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.003 0.001 HIS R 192 PHE 0.025 0.001 PHE R 493 TYR 0.019 0.001 TYR A 308 ARG 0.008 0.001 ARG B 42 ********************** 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 285 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 255 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.7085 (ttm) cc_final: 0.6818 (mtt) REVERT: A 229 ASP cc_start: 0.7728 (p0) cc_final: 0.7407 (p0) REVERT: A 267 TRP cc_start: 0.8800 (t-100) cc_final: 0.8443 (t-100) REVERT: A 360 GLU cc_start: 0.7743 (mp0) cc_final: 0.7426 (mp0) REVERT: B 33 ILE cc_start: 0.6610 (tt) cc_final: 0.6325 (tp) REVERT: B 51 LEU cc_start: 0.8819 (mp) cc_final: 0.8522 (mp) REVERT: B 54 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.7441 (t70) REVERT: B 130 GLU cc_start: 0.6648 (mp0) cc_final: 0.6328 (mt-10) REVERT: B 155 ASN cc_start: 0.8288 (t0) cc_final: 0.7949 (t0) REVERT: B 189 SER cc_start: 0.7935 (p) cc_final: 0.7529 (t) REVERT: B 259 GLN cc_start: 0.7755 (pt0) cc_final: 0.7503 (pt0) REVERT: B 260 GLU cc_start: 0.6708 (tt0) cc_final: 0.6386 (tt0) REVERT: B 293 ASN cc_start: 0.8380 (p0) cc_final: 0.8073 (p0) REVERT: G 20 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8585 (tppp) REVERT: G 25 ILE cc_start: 0.8602 (tp) cc_final: 0.8320 (pt) REVERT: G 58 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7449 (mp0) REVERT: R 108 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7290 (p) REVERT: R 143 LYS cc_start: 0.4262 (pttt) cc_final: 0.3885 (pttm) REVERT: R 253 SER cc_start: 0.8794 (t) cc_final: 0.8188 (p) REVERT: R 262 ARG cc_start: 0.7155 (tpt90) cc_final: 0.6603 (tpt90) REVERT: R 405 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7588 (t0) REVERT: R 484 ILE cc_start: 0.8572 (mm) cc_final: 0.8162 (tp) REVERT: R 559 MET cc_start: 0.5908 (tpt) cc_final: 0.5450 (tmm) REVERT: R 633 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: X 84 CYS cc_start: 0.4770 (OUTLIER) cc_final: 0.4513 (m) REVERT: Y 104 LYS cc_start: 0.5694 (tptp) cc_final: 0.4758 (tttt) outliers start: 30 outliers final: 23 residues processed: 271 average time/residue: 0.2672 time to fit residues: 97.9919 Evaluate side-chains 275 residues out of total 1208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 247 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 351 ASN Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 474 LEU Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 522 THR Chi-restraints excluded: chain R residue 543 CYS Chi-restraints excluded: chain R residue 633 ASP Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Y residue 34 CYS Chi-restraints excluded: chain Y residue 44 VAL Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 90 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 0.0170 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 0.0170 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 227 GLN B 44 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.127274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.115591 restraints weight = 20997.250| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.44 r_work: 0.3601 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 11076 Z= 0.276 Angle : 0.912 59.172 15015 Z= 0.512 Chirality : 0.044 0.189 1714 Planarity : 0.004 0.070 1917 Dihedral : 5.288 37.354 1524 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.34 % Allowed : 23.22 % Favored : 74.44 % 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: 2.23 (0.27), residues: 389 sheet: -1.36 (0.29), residues: 296 loop : -0.30 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.003 0.001 HIS R 160 PHE 0.023 0.001 PHE R 493 TYR 0.015 0.001 TYR A 308 ARG 0.011 0.001 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3033.11 seconds wall clock time: 55 minutes 17.62 seconds (3317.62 seconds total)