Starting phenix.real_space_refine (version: dev) on Fri Mar 17 17:16:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkp_14764/03_2023/7zkp_14764_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkp_14764/03_2023/7zkp_14764.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/7zkp_14764/03_2023/7zkp_14764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkp_14764/03_2023/7zkp_14764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkp_14764/03_2023/7zkp_14764_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkp_14764/03_2023/7zkp_14764_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= 0.010 sd= 0.099 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 Process input model Symmetric amino acids flipped Residue "X GLU 124": "OE1" <-> "OE2" Residue "2 GLU 433": "OE1" <-> "OE2" Residue "6 GLU 84": "OE1" <-> "OE2" Residue "b TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 828": "OE1" <-> "OE2" Residue "A GLU 143": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 19929 Number of models: 1 Model: "" Number of chains: 19 Chain: "D" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 681 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "L" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1345 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "W" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 744 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "X" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1274 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "1" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2426 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 290} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3776 Classifications: {'peptide': 469} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 461} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 909 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "6" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1453 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 3, 'TRANS': 180} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 622 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 10, 'TRANS': 65} Chain: "b" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 490 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "9" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "C" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2763 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1749 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 64 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 3 Chain: "1" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 126 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Chain: "b" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'T7X': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Time building chain proxies: 11.09, per 1000 atoms: 0.56 Number of scatterers: 19929 At special positions: 0 Unit cell: (129.171, 118.307, 150.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 8 15.00 O 3535 8.00 N 3145 7.00 C 13161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS U 46 " - pdb=" SG CYS U 78 " distance=2.03 Simple disulfide: pdb=" SG CYS U 56 " - pdb=" SG CYS U 68 " distance=2.04 Simple disulfide: pdb=" SG CYS U 90 " - pdb=" SG CYS U 121 " distance=2.04 Simple disulfide: pdb=" SG CYS U 100 " - pdb=" SG CYS U 111 " distance=2.03 Simple disulfide: pdb=" SG CYS 9 15 " - pdb=" SG CYS 9 47 " distance=2.03 Simple disulfide: pdb=" SG CYS 9 25 " - pdb=" SG CYS 9 37 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.20 Conformation dependent library (CDL) restraints added in 2.8 seconds 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4630 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 4 sheets defined 62.8% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'D' and resid 5 through 33 Proline residue: D 10 - end of helix Processing helix chain 'D' and resid 44 through 57 Processing helix chain 'D' and resid 72 through 75 Processing helix chain 'L' and resid 3 through 18 Processing helix chain 'L' and resid 22 through 47 Processing helix chain 'L' and resid 50 through 78 Processing helix chain 'U' and resid 32 through 60 removed outlier: 5.235A pdb=" N TYR U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N PHE U 41 " --> pdb=" O SER U 37 " (cutoff:3.500A) Proline residue: U 48 - end of helix Processing helix chain 'U' and resid 64 through 67 No H-bonds generated for 'chain 'U' and resid 64 through 67' Processing helix chain 'U' and resid 69 through 87 Processing helix chain 'U' and resid 91 through 104 Processing helix chain 'U' and resid 108 through 125 removed outlier: 3.659A pdb=" N CYS U 111 " --> pdb=" O LEU U 108 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG U 112 " --> pdb=" O SER U 109 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LYS U 113 " --> pdb=" O GLY U 110 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA U 114 " --> pdb=" O CYS U 111 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS U 125 " --> pdb=" O VAL U 122 " (cutoff:3.500A) Processing helix chain 'U' and resid 142 through 144 No H-bonds generated for 'chain 'U' and resid 142 through 144' Processing helix chain 'U' and resid 157 through 169 Processing helix chain 'W' and resid 32 through 95 removed outlier: 3.527A pdb=" N LEU W 69 " --> pdb=" O ALA W 65 " (cutoff:3.500A) Proline residue: W 71 - end of helix Processing helix chain 'X' and resid 28 through 33 Processing helix chain 'X' and resid 37 through 60 Proline residue: X 51 - end of helix Processing helix chain 'X' and resid 72 through 98 Processing helix chain 'X' and resid 105 through 121 Processing helix chain 'X' and resid 133 through 143 Processing helix chain 'X' and resid 146 through 149 Processing helix chain '1' and resid 3 through 33 removed outlier: 3.766A pdb=" N THR 1 23 " --> pdb=" O VAL 1 19 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 46 through 57 removed outlier: 3.558A pdb=" N ALA 1 52 " --> pdb=" O LEU 1 48 " (cutoff:3.500A) Processing helix chain '1' and resid 70 through 88 Proline residue: 1 77 - end of helix removed outlier: 4.239A pdb=" N TRP 1 88 " --> pdb=" O ALA 1 84 " (cutoff:3.500A) Processing helix chain '1' and resid 105 through 126 removed outlier: 4.096A pdb=" N VAL 1 117 " --> pdb=" O GLY 1 113 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N PHE 1 118 " --> pdb=" O SER 1 114 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLY 1 119 " --> pdb=" O LEU 1 115 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N SER 1 120 " --> pdb=" O GLY 1 116 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU 1 121 " --> pdb=" O VAL 1 117 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 160 removed outlier: 3.706A pdb=" N ILE 1 149 " --> pdb=" O SER 1 145 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE 1 160 " --> pdb=" O ILE 1 156 " (cutoff:3.500A) Processing helix chain '1' and resid 166 through 174 removed outlier: 3.924A pdb=" N ARG 1 174 " --> pdb=" O ILE 1 170 " (cutoff:3.500A) Processing helix chain '1' and resid 178 through 181 No H-bonds generated for 'chain '1' and resid 178 through 181' Processing helix chain '1' and resid 183 through 196 Processing helix chain '1' and resid 223 through 245 Processing helix chain '1' and resid 256 through 262 Processing helix chain '1' and resid 268 through 297 Processing helix chain '1' and resid 305 through 314 removed outlier: 3.645A pdb=" N CYS 1 312 " --> pdb=" O LEU 1 308 " (cutoff:3.500A) Processing helix chain '1' and resid 316 through 333 Proline residue: 1 328 - end of helix Processing helix chain '2' and resid 3 through 14 Processing helix chain '2' and resid 18 through 38 removed outlier: 4.367A pdb=" N ARG 2 22 " --> pdb=" O SER 2 19 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU 2 38 " --> pdb=" O VAL 2 35 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 49 removed outlier: 3.957A pdb=" N LEU 2 47 " --> pdb=" O LEU 2 44 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN 2 48 " --> pdb=" O LEU 2 45 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN 2 49 " --> pdb=" O PHE 2 46 " (cutoff:3.500A) Processing helix chain '2' and resid 63 through 84 Processing helix chain '2' and resid 91 through 96 Processing helix chain '2' and resid 103 through 118 Processing helix chain '2' and resid 123 through 142 Processing helix chain '2' and resid 148 through 179 removed outlier: 3.565A pdb=" N ALA 2 153 " --> pdb=" O LYS 2 149 " (cutoff:3.500A) Processing helix chain '2' and resid 184 through 186 No H-bonds generated for 'chain '2' and resid 184 through 186' Processing helix chain '2' and resid 189 through 194 Processing helix chain '2' and resid 198 through 212 removed outlier: 3.793A pdb=" N ILE 2 212 " --> pdb=" O LEU 2 208 " (cutoff:3.500A) Processing helix chain '2' and resid 219 through 227 Processing helix chain '2' and resid 230 through 236 removed outlier: 4.356A pdb=" N TYR 2 235 " --> pdb=" O LEU 2 231 " (cutoff:3.500A) Processing helix chain '2' and resid 239 through 251 Processing helix chain '2' and resid 258 through 277 removed outlier: 3.729A pdb=" N LEU 2 276 " --> pdb=" O SER 2 272 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU 2 277 " --> pdb=" O VAL 2 273 " (cutoff:3.500A) Processing helix chain '2' and resid 281 through 301 removed outlier: 3.721A pdb=" N LEU 2 299 " --> pdb=" O TYR 2 295 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU 2 300 " --> pdb=" O MET 2 296 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU 2 301 " --> pdb=" O MET 2 297 " (cutoff:3.500A) Processing helix chain '2' and resid 306 through 333 removed outlier: 3.569A pdb=" N ILE 2 331 " --> pdb=" O ILE 2 327 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYR 2 332 " --> pdb=" O ILE 2 328 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TYR 2 333 " --> pdb=" O PHE 2 329 " (cutoff:3.500A) Processing helix chain '2' and resid 347 through 350 Processing helix chain '2' and resid 353 through 355 No H-bonds generated for 'chain '2' and resid 353 through 355' Processing helix chain '2' and resid 358 through 372 Processing helix chain '2' and resid 378 through 392 Processing helix chain '2' and resid 396 through 420 removed outlier: 3.786A pdb=" N LEU 2 411 " --> pdb=" O LEU 2 407 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR 2 412 " --> pdb=" O ILE 2 408 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU 2 416 " --> pdb=" O TYR 2 412 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU 2 417 " --> pdb=" O TYR 2 413 " (cutoff:3.500A) Processing helix chain '2' and resid 437 through 467 removed outlier: 5.600A pdb=" N PHE 2 454 " --> pdb=" O ILE 2 450 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE 2 455 " --> pdb=" O THR 2 451 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TYR 2 456 " --> pdb=" O PHE 2 452 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASN 2 457 " --> pdb=" O GLY 2 453 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER 2 458 " --> pdb=" O PHE 2 454 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU 2 459 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 26 Proline residue: 3 12 - end of helix removed outlier: 4.233A pdb=" N LEU 3 25 " --> pdb=" O VAL 3 21 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA 3 26 " --> pdb=" O ASN 3 22 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 78 removed outlier: 4.323A pdb=" N LEU 3 64 " --> pdb=" O ALA 3 60 " (cutoff:3.500A) Proline residue: 3 65 - end of helix removed outlier: 3.686A pdb=" N LEU 3 73 " --> pdb=" O GLU 3 69 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU 3 74 " --> pdb=" O ILE 3 70 " (cutoff:3.500A) Proline residue: 3 75 - end of helix Processing helix chain '3' and resid 84 through 107 removed outlier: 3.514A pdb=" N GLY 3 101 " --> pdb=" O ILE 3 97 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 6 No H-bonds generated for 'chain '6' and resid 3 through 6' Processing helix chain '6' and resid 8 through 24 Processing helix chain '6' and resid 29 through 50 Processing helix chain '6' and resid 53 through 65 removed outlier: 3.724A pdb=" N ILE 6 64 " --> pdb=" O ILE 6 60 " (cutoff:3.500A) Processing helix chain '6' and resid 67 through 80 Processing helix chain '6' and resid 91 through 109 Proline residue: 6 95 - end of helix Processing helix chain '6' and resid 112 through 117 Processing helix chain '6' and resid 119 through 127 Processing helix chain '6' and resid 146 through 155 Processing helix chain '6' and resid 159 through 180 Proline residue: 6 176 - end of helix Processing helix chain 'g' and resid 12 through 22 Processing helix chain 'g' and resid 24 through 50 removed outlier: 3.605A pdb=" N GLY g 36 " --> pdb=" O ILE g 32 " (cutoff:3.500A) Proline residue: g 37 - end of helix Proline residue: g 45 - end of helix Processing helix chain 'b' and resid 3 through 24 Processing helix chain 'b' and resid 33 through 63 Processing helix chain '9' and resid 16 through 28 Processing helix chain '9' and resid 32 through 49 removed outlier: 4.345A pdb=" N ALA 9 35 " --> pdb=" O LYS 9 32 " (cutoff:3.500A) Proline residue: 9 39 - end of helix Processing helix chain '9' and resid 51 through 66 Processing helix chain '9' and resid 81 through 83 No H-bonds generated for 'chain '9' and resid 81 through 83' Processing helix chain 'C' and resid 510 through 524 removed outlier: 3.905A pdb=" N ALA C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 522 " --> pdb=" O GLN C 518 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 537 removed outlier: 3.600A pdb=" N THR C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET C 534 " --> pdb=" O PHE C 530 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN C 535 " --> pdb=" O TYR C 531 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C 536 " --> pdb=" O THR C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 556 through 566 removed outlier: 3.564A pdb=" N TYR C 565 " --> pdb=" O HIS C 561 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 566 " --> pdb=" O ASP C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 585 Processing helix chain 'C' and resid 590 through 602 removed outlier: 3.509A pdb=" N PHE C 600 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA C 601 " --> pdb=" O LYS C 598 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN C 602 " --> pdb=" O PHE C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 623 Processing helix chain 'C' and resid 631 through 641 Processing helix chain 'C' and resid 647 through 659 removed outlier: 3.550A pdb=" N LYS C 651 " --> pdb=" O LYS C 647 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 659 " --> pdb=" O GLU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 679 Processing helix chain 'C' and resid 683 through 694 removed outlier: 3.522A pdb=" N GLN C 687 " --> pdb=" O LEU C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 713 Processing helix chain 'C' and resid 718 through 731 Proline residue: C 729 - end of helix Processing helix chain 'C' and resid 737 through 749 removed outlier: 3.886A pdb=" N GLN C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR C 743 " --> pdb=" O ASN C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 766 removed outlier: 3.578A pdb=" N LEU C 757 " --> pdb=" O TYR C 753 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 758 " --> pdb=" O ARG C 754 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU C 764 " --> pdb=" O THR C 760 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE C 765 " --> pdb=" O LYS C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 781 removed outlier: 3.797A pdb=" N ALA C 778 " --> pdb=" O LYS C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 799 removed outlier: 3.582A pdb=" N GLU C 793 " --> pdb=" O LYS C 789 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TRP C 795 " --> pdb=" O GLU C 791 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLU C 797 " --> pdb=" O GLU C 793 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS C 798 " --> pdb=" O GLN C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 808 removed outlier: 3.653A pdb=" N LEU C 805 " --> pdb=" O PRO C 801 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 806 " --> pdb=" O GLU C 802 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU C 807 " --> pdb=" O MET C 803 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 808 " --> pdb=" O TRP C 804 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 801 through 808' Processing helix chain 'C' and resid 827 through 843 removed outlier: 3.540A pdb=" N GLU C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 29 Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing sheet with id= A, first strand: chain '2' and resid 52 through 54 Processing sheet with id= B, first strand: chain 'A' and resid 30 through 34 removed outlier: 5.426A pdb=" N VAL A 176 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN A 122 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 176 " --> pdb=" O ASN A 120 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN A 120 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE A 178 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE A 118 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER A 123 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP A 130 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 43 through 49 removed outlier: 3.527A pdb=" N ASN A 45 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 61 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 191 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG A 109 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE A 195 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLU A 107 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.412A pdb=" N ILE A 195 " --> pdb=" O LEU A 18 " (cutoff:3.500A) 1075 hydrogen bonds defined for protein. 3042 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: 5.51 Time building geometry restraints manager: 8.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3068 1.31 - 1.44: 5542 1.44 - 1.57: 11617 1.57 - 1.70: 20 1.70 - 1.84: 134 Bond restraints: 20381 Sorted by residual: bond pdb=" C LEU X 131 " pdb=" O LEU X 131 " ideal model delta sigma weight residual 1.234 1.176 0.058 1.17e-02 7.31e+03 2.46e+01 bond pdb=" CB PLC 1 401 " pdb=" O3 PLC 1 401 " ideal model delta sigma weight residual 1.327 1.418 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C11 CPL 2 501 " pdb=" O3 CPL 2 501 " ideal model delta sigma weight residual 1.327 1.417 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C' PLC 1 401 " pdb=" O2 PLC 1 401 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.00e+01 bond pdb=" CA SER X 130 " pdb=" CB SER X 130 " ideal model delta sigma weight residual 1.532 1.455 0.078 1.79e-02 3.12e+03 1.89e+01 ... (remaining 20376 not shown) Histogram of bond angle deviations from ideal: 94.23 - 105.88: 401 105.88 - 117.54: 14620 117.54 - 129.20: 12485 129.20 - 140.85: 110 140.85 - 152.51: 1 Bond angle restraints: 27617 Sorted by residual: angle pdb=" C39 CPL 2 501 " pdb=" C40 CPL 2 501 " pdb=" C41 CPL 2 501 " ideal model delta sigma weight residual 127.51 152.51 -25.00 3.00e+00 1.11e-01 6.94e+01 angle pdb=" C38 CPL 2 501 " pdb=" C39 CPL 2 501 " pdb=" C40 CPL 2 501 " ideal model delta sigma weight residual 127.82 111.74 16.08 3.00e+00 1.11e-01 2.87e+01 angle pdb=" O3P PLC 1 401 " pdb=" P PLC 1 401 " pdb=" O4P PLC 1 401 " ideal model delta sigma weight residual 93.62 109.53 -15.91 3.00e+00 1.11e-01 2.81e+01 angle pdb=" N ILE 3 23 " pdb=" CA ILE 3 23 " pdb=" C ILE 3 23 " ideal model delta sigma weight residual 113.07 105.90 7.17 1.36e+00 5.41e-01 2.78e+01 angle pdb=" O3P CPL 2 501 " pdb=" P CPL 2 501 " pdb=" O4P CPL 2 501 " ideal model delta sigma weight residual 93.29 108.55 -15.26 3.00e+00 1.11e-01 2.59e+01 ... (remaining 27612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 11811 35.63 - 71.26: 239 71.26 - 106.89: 13 106.89 - 142.52: 2 142.52 - 178.15: 1 Dihedral angle restraints: 12066 sinusoidal: 4868 harmonic: 7198 Sorted by residual: dihedral pdb=" N SER X 130 " pdb=" C SER X 130 " pdb=" CA SER X 130 " pdb=" CB SER X 130 " ideal model delta harmonic sigma weight residual 122.80 109.23 13.57 0 2.50e+00 1.60e-01 2.95e+01 dihedral pdb=" N CPL 2 501 " pdb=" C4 CPL 2 501 " pdb=" C5 CPL 2 501 " pdb=" O4P CPL 2 501 " ideal model delta sinusoidal sigma weight residual 288.92 110.77 178.15 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C SER X 130 " pdb=" N SER X 130 " pdb=" CA SER X 130 " pdb=" CB SER X 130 " ideal model delta harmonic sigma weight residual -122.60 -111.24 -11.36 0 2.50e+00 1.60e-01 2.06e+01 ... (remaining 12063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2602 0.054 - 0.107: 520 0.107 - 0.161: 43 0.161 - 0.214: 10 0.214 - 0.268: 3 Chirality restraints: 3178 Sorted by residual: chirality pdb=" CA THR X 128 " pdb=" N THR X 128 " pdb=" C THR X 128 " pdb=" CB THR X 128 " both_signs ideal model delta sigma weight residual False 2.53 2.79 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA SER X 130 " pdb=" N SER X 130 " pdb=" C SER X 130 " pdb=" CB SER X 130 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C2 PLC 1 401 " pdb=" C1 PLC 1 401 " pdb=" C3 PLC 1 401 " pdb=" O2 PLC 1 401 " both_signs ideal model delta sigma weight residual False -2.31 -2.53 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 3175 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 23 " 0.077 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO A 24 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 24 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 24 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 804 " 0.021 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP C 804 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP C 804 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 804 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 804 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 804 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 804 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 804 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 804 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 804 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY X 127 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C GLY X 127 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY X 127 " -0.015 2.00e-02 2.50e+03 pdb=" N THR X 128 " -0.013 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 312 2.68 - 3.23: 19973 3.23 - 3.79: 32375 3.79 - 4.34: 43832 4.34 - 4.90: 70738 Nonbonded interactions: 167230 Sorted by model distance: nonbonded pdb=" O PHE X 151 " pdb=" OH TYR 2 73 " model vdw 2.119 2.440 nonbonded pdb=" OD1 ASP A 130 " pdb=" ND2 ASN A 158 " model vdw 2.137 2.520 nonbonded pdb=" NH2 ARG X 30 " pdb=" OD1 ASP X 111 " model vdw 2.146 2.520 nonbonded pdb=" NH1 ARG X 30 " pdb=" OE1 GLN X 114 " model vdw 2.166 2.520 nonbonded pdb=" O ILE 2 10 " pdb=" OG SER 2 14 " model vdw 2.170 2.440 ... (remaining 167225 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 80 5.16 5 C 13161 2.51 5 N 3145 2.21 5 O 3535 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=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.970 Check model and map are aligned: 0.310 Process input model: 50.240 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 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 : 0.004 0.091 20381 Z= 0.285 Angle : 0.731 25.001 27617 Z= 0.368 Chirality : 0.042 0.268 3178 Planarity : 0.005 0.115 3396 Dihedral : 14.424 178.146 7418 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.31 % Favored : 95.52 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.09 % 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: 0.98 (0.17), residues: 2413 helix: 1.43 (0.13), residues: 1549 sheet: -1.27 (0.62), residues: 70 loop : -0.65 (0.23), residues: 794 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 603 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 605 average time/residue: 0.3445 time to fit residues: 308.1790 Evaluate side-chains 303 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 2.131 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 5.9990 chunk 180 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 186 optimal weight: 0.3980 chunk 72 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 HIS U 119 ASN 1 69 ASN 1 310 ASN 2 29 ASN ** 2 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 338 ASN 2 349 GLN 3 53 ASN 3 85 ASN ** 3 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 GLN C 704 ASN A 72 ASN A 88 GLN A 165 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 20381 Z= 0.271 Angle : 0.657 12.825 27617 Z= 0.331 Chirality : 0.042 0.192 3178 Planarity : 0.005 0.072 3396 Dihedral : 9.803 149.698 2866 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.39 % Favored : 95.44 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 0.93 (0.17), residues: 2413 helix: 1.41 (0.13), residues: 1549 sheet: -0.84 (0.62), residues: 73 loop : -0.76 (0.23), residues: 791 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 299 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 26 residues processed: 335 average time/residue: 0.3121 time to fit residues: 162.0034 Evaluate side-chains 274 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 248 time to evaluate : 2.295 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2156 time to fit residues: 13.1162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 216 optimal weight: 0.0470 chunk 233 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN D 33 ASN W 114 HIS 2 304 ASN 2 349 GLN 3 107 ASN C 787 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 20381 Z= 0.179 Angle : 0.537 8.666 27617 Z= 0.274 Chirality : 0.039 0.166 3178 Planarity : 0.004 0.060 3396 Dihedral : 9.346 161.384 2866 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.85 % Favored : 95.98 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.18), residues: 2413 helix: 1.72 (0.13), residues: 1552 sheet: -0.77 (0.61), residues: 72 loop : -0.68 (0.23), residues: 789 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 278 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 9 residues processed: 295 average time/residue: 0.3180 time to fit residues: 145.6072 Evaluate side-chains 249 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 240 time to evaluate : 2.284 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2261 time to fit residues: 6.8189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 145 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN L 43 ASN U 8 HIS U 169 ASN X 145 HIS ** 1 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 ASN 2 198 ASN C 522 GLN A 72 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 20381 Z= 0.221 Angle : 0.549 10.463 27617 Z= 0.277 Chirality : 0.039 0.186 3178 Planarity : 0.004 0.055 3396 Dihedral : 8.953 155.691 2866 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.02 % Favored : 95.81 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.17), residues: 2413 helix: 1.75 (0.13), residues: 1554 sheet: -0.93 (0.56), residues: 82 loop : -0.73 (0.24), residues: 777 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 273 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 19 residues processed: 297 average time/residue: 0.3183 time to fit residues: 146.9443 Evaluate side-chains 266 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 247 time to evaluate : 2.365 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2018 time to fit residues: 10.0376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 10.0000 chunk 130 optimal weight: 0.1980 chunk 3 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 117 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 169 ASN 1 142 GLN 2 50 GLN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 20381 Z= 0.196 Angle : 0.530 9.047 27617 Z= 0.269 Chirality : 0.038 0.164 3178 Planarity : 0.004 0.053 3396 Dihedral : 8.772 157.734 2866 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.85 % Favored : 95.98 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.17), residues: 2413 helix: 1.82 (0.13), residues: 1552 sheet: -0.66 (0.60), residues: 68 loop : -0.77 (0.23), residues: 793 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 278 time to evaluate : 2.468 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 297 average time/residue: 0.3327 time to fit residues: 154.9309 Evaluate side-chains 259 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 248 time to evaluate : 2.290 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1960 time to fit residues: 7.2555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 76 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 78 HIS U 169 ASN 1 173 GLN 2 29 ASN b 52 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 20381 Z= 0.162 Angle : 0.518 11.397 27617 Z= 0.259 Chirality : 0.038 0.255 3178 Planarity : 0.004 0.050 3396 Dihedral : 8.552 157.047 2866 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.85 % Favored : 95.98 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2413 helix: 1.99 (0.13), residues: 1542 sheet: -0.76 (0.60), residues: 70 loop : -0.76 (0.23), residues: 801 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 268 time to evaluate : 2.386 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 281 average time/residue: 0.3368 time to fit residues: 147.9921 Evaluate side-chains 259 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 245 time to evaluate : 2.250 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3170 time to fit residues: 10.3592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 168 optimal weight: 0.4980 chunk 130 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 169 ASN 1 142 GLN 2 252 ASN b 52 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 HIS ** C 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 20381 Z= 0.242 Angle : 0.561 14.025 27617 Z= 0.282 Chirality : 0.039 0.217 3178 Planarity : 0.004 0.080 3396 Dihedral : 8.623 158.674 2866 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.98 % Favored : 95.86 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.17), residues: 2413 helix: 1.93 (0.13), residues: 1541 sheet: -0.74 (0.63), residues: 68 loop : -0.70 (0.23), residues: 804 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 269 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 279 average time/residue: 0.3228 time to fit residues: 139.7529 Evaluate side-chains 260 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 248 time to evaluate : 2.315 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2131 time to fit residues: 7.7333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 169 ASN 2 29 ASN b 52 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 20381 Z= 0.227 Angle : 0.548 11.514 27617 Z= 0.275 Chirality : 0.039 0.205 3178 Planarity : 0.004 0.054 3396 Dihedral : 8.600 158.878 2866 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.06 % Favored : 95.81 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.17), residues: 2413 helix: 1.90 (0.13), residues: 1547 sheet: -0.81 (0.63), residues: 68 loop : -0.69 (0.23), residues: 798 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 267 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 277 average time/residue: 0.3388 time to fit residues: 146.5792 Evaluate side-chains 253 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 244 time to evaluate : 1.888 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1958 time to fit residues: 6.2984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 10.0000 chunk 219 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 chunk 213 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 252 ASN ** 3 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 20381 Z= 0.191 Angle : 0.531 9.196 27617 Z= 0.269 Chirality : 0.038 0.226 3178 Planarity : 0.004 0.055 3396 Dihedral : 8.457 158.562 2866 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.02 % Favored : 95.86 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.18), residues: 2413 helix: 1.97 (0.13), residues: 1545 sheet: -0.99 (0.64), residues: 64 loop : -0.66 (0.23), residues: 804 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 259 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 266 average time/residue: 0.3256 time to fit residues: 136.4080 Evaluate side-chains 248 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 243 time to evaluate : 2.185 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2146 time to fit residues: 5.2555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 237 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 188 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 115 optimal weight: 0.0980 chunk 149 optimal weight: 0.8980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 173 GLN 2 29 ASN ** 3 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 20381 Z= 0.206 Angle : 0.550 13.938 27617 Z= 0.278 Chirality : 0.039 0.240 3178 Planarity : 0.004 0.055 3396 Dihedral : 8.383 158.663 2866 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.27 % Favored : 95.61 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2413 helix: 1.92 (0.13), residues: 1546 sheet: -0.90 (0.60), residues: 76 loop : -0.57 (0.23), residues: 791 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 257 time to evaluate : 2.436 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 262 average time/residue: 0.3247 time to fit residues: 133.9947 Evaluate side-chains 250 residues out of total 2138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 245 time to evaluate : 2.270 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2607 time to fit residues: 5.2832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 189 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 ASN C 739 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.136157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.100817 restraints weight = 29187.028| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.26 r_work: 0.3178 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 20381 Z= 0.267 Angle : 0.582 12.876 27617 Z= 0.293 Chirality : 0.040 0.195 3178 Planarity : 0.004 0.056 3396 Dihedral : 8.442 159.515 2866 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.35 % Favored : 95.48 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.17), residues: 2413 helix: 1.77 (0.13), residues: 1556 sheet: -0.80 (0.63), residues: 68 loop : -0.60 (0.23), residues: 789 Sorry: There was an error with writing 7zkp_14764_updated_real_space_refined_001.pdb. [Errno 28] No space left on device