Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 23:52:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fho_29097/04_2023/8fho_29097_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fho_29097/04_2023/8fho_29097.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fho_29097/04_2023/8fho_29097_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fho_29097/04_2023/8fho_29097_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fho_29097/04_2023/8fho_29097_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fho_29097/04_2023/8fho_29097.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fho_29097/04_2023/8fho_29097.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fho_29097/04_2023/8fho_29097_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fho_29097/04_2023/8fho_29097_updated.pdb" } resolution = 2.95 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= -0.001 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 6 5.49 5 S 81 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 8852 2.51 5 N 2274 2.21 5 O 2401 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A ASP 965": "OD1" <-> "OD2" Residue "A TYR 1019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 504": "OE1" <-> "OE2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 756": "OD1" <-> "OD2" Residue "B GLU 778": "OE1" <-> "OE2" Residue "B TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 873": "OD1" <-> "OD2" Residue "B GLU 892": "OE1" <-> "OE2" Residue "B PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 943": "OD1" <-> "OD2" Residue "B TYR 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 969": "OD1" <-> "OD2" Residue "C ASP 147": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 13624 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 847, 6630 Classifications: {'peptide': 847} Link IDs: {'PTRANS': 37, 'TRANS': 809} Chain breaks: 2 Chain: "B" Number of atoms: 6643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 847, 6643 Classifications: {'peptide': 847} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 810} Chain breaks: 2 Chain: "C" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 237 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' NA': 1, 'ATP': 1, 'XZF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' NA': 1, 'ATP': 1, 'XZF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.98, per 1000 atoms: 0.51 Number of scatterers: 13624 At special positions: 0 Unit cell: (110.94, 145.34, 113.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 2 17.00 S 81 16.00 P 6 15.00 Na 2 11.00 F 6 9.00 O 2401 8.00 N 2274 7.00 C 8852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 421 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 436 " distance=2.07 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 421 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 436 " distance=2.02 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: 5.49 Conformation dependent library (CDL) restraints added in 2.0 seconds 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3172 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 3 sheets defined 53.8% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 154 through 157 No H-bonds generated for 'chain 'A' and resid 154 through 157' Processing helix chain 'A' and resid 159 through 194 removed outlier: 7.026A pdb=" N ILE A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N VAL A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 220 through 247 removed outlier: 3.853A pdb=" N ALA A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 276 removed outlier: 3.517A pdb=" N THR A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 270 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 303 removed outlier: 3.938A pdb=" N SER A 283 " --> pdb=" O MET A 279 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 313 No H-bonds generated for 'chain 'A' and resid 310 through 313' Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 340 through 350 removed outlier: 3.794A pdb=" N ILE A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.744A pdb=" N SER A 361 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLY A 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 395 Proline residue: A 372 - end of helix removed outlier: 3.571A pdb=" N LEU A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 390 " --> pdb=" O TYR A 386 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 446 through 449 No H-bonds generated for 'chain 'A' and resid 446 through 449' Processing helix chain 'A' and resid 454 through 485 removed outlier: 3.564A pdb=" N THR A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 496 Processing helix chain 'A' and resid 506 through 522 removed outlier: 3.570A pdb=" N LEU A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 511 " --> pdb=" O ARG A 507 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 535 Processing helix chain 'A' and resid 537 through 553 removed outlier: 3.679A pdb=" N LEU A 542 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 584 removed outlier: 3.627A pdb=" N ALA A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 606 removed outlier: 3.733A pdb=" N LEU A 590 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 591 " --> pdb=" O TRP A 587 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 633 removed outlier: 3.557A pdb=" N SER A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N TYR A 621 " --> pdb=" O GLN A 617 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASN A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'A' and resid 656 through 665 removed outlier: 3.988A pdb=" N PHE A 665 " --> pdb=" O PHE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 702 removed outlier: 3.934A pdb=" N LYS A 698 " --> pdb=" O GLY A 695 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP A 699 " --> pdb=" O HIS A 696 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 700 " --> pdb=" O THR A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 Processing helix chain 'A' and resid 751 through 766 removed outlier: 3.777A pdb=" N GLU A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP A 756 " --> pdb=" O ALA A 752 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 851 Proline residue: A 847 - end of helix Processing helix chain 'A' and resid 854 through 856 No H-bonds generated for 'chain 'A' and resid 854 through 856' Processing helix chain 'A' and resid 881 through 884 No H-bonds generated for 'chain 'A' and resid 881 through 884' Processing helix chain 'A' and resid 905 through 918 Proline residue: A 917 - end of helix Processing helix chain 'A' and resid 927 through 934 removed outlier: 3.837A pdb=" N MET A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 966 removed outlier: 3.887A pdb=" N ARG A 950 " --> pdb=" O ILE A 946 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL A 951 " --> pdb=" O THR A 947 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS A 952 " --> pdb=" O LYS A 948 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 953 " --> pdb=" O ASN A 949 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN A 960 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU A 961 " --> pdb=" O VAL A 957 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 962 " --> pdb=" O ARG A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 996 Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 154 through 157 No H-bonds generated for 'chain 'B' and resid 154 through 157' Processing helix chain 'B' and resid 159 through 166 Processing helix chain 'B' and resid 168 through 193 removed outlier: 3.543A pdb=" N ILE B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 210 removed outlier: 4.125A pdb=" N LEU B 206 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 208 " --> pdb=" O PHE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 249 removed outlier: 3.873A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU B 248 " --> pdb=" O ASP B 244 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 277 removed outlier: 3.621A pdb=" N ILE B 260 " --> pdb=" O PRO B 256 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 303 removed outlier: 3.964A pdb=" N VAL B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE B 290 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 313 No H-bonds generated for 'chain 'B' and resid 310 through 313' Processing helix chain 'B' and resid 322 through 329 Processing helix chain 'B' and resid 340 through 350 removed outlier: 3.913A pdb=" N ILE B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) Proline residue: B 349 - end of helix Processing helix chain 'B' and resid 358 through 363 removed outlier: 3.833A pdb=" N SER B 361 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLY B 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 393 removed outlier: 3.606A pdb=" N ILE B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Proline residue: B 372 - end of helix removed outlier: 3.562A pdb=" N LEU B 376 " --> pdb=" O PRO B 372 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 423 Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.831A pdb=" N GLN B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 454 through 484 removed outlier: 3.503A pdb=" N THR B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 522 removed outlier: 4.747A pdb=" N LEU B 511 " --> pdb=" O ARG B 507 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 552 removed outlier: 3.765A pdb=" N PHE B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 584 removed outlier: 3.806A pdb=" N ALA B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE B 582 " --> pdb=" O VAL B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 604 removed outlier: 3.538A pdb=" N LEU B 590 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 591 " --> pdb=" O TRP B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 628 Processing helix chain 'B' and resid 630 through 632 No H-bonds generated for 'chain 'B' and resid 630 through 632' Processing helix chain 'B' and resid 638 through 640 No H-bonds generated for 'chain 'B' and resid 638 through 640' Processing helix chain 'B' and resid 656 through 665 removed outlier: 3.740A pdb=" N THR B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE B 665 " --> pdb=" O PHE B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 702 Processing helix chain 'B' and resid 717 through 727 removed outlier: 3.781A pdb=" N ILE B 723 " --> pdb=" O ARG B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 766 removed outlier: 3.843A pdb=" N GLU B 755 " --> pdb=" O PRO B 751 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 842 through 850 Proline residue: B 847 - end of helix Processing helix chain 'B' and resid 872 through 885 removed outlier: 3.706A pdb=" N ALA B 878 " --> pdb=" O GLN B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 914 removed outlier: 3.842A pdb=" N ARG B 910 " --> pdb=" O GLU B 906 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 934 removed outlier: 3.596A pdb=" N MET B 933 " --> pdb=" O THR B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 947 Processing helix chain 'B' and resid 951 through 966 removed outlier: 3.706A pdb=" N GLN B 956 " --> pdb=" O LYS B 952 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 961 " --> pdb=" O VAL B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 998 removed outlier: 4.026A pdb=" N SER B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 Processing sheet with id= A, first strand: chain 'A' and resid 672 through 675 removed outlier: 6.749A pdb=" N CYS A 645 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLY A 675 " --> pdb=" O CYS A 645 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 647 " --> pdb=" O GLY A 675 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 737 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU A 648 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL A 739 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY A 770 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL A 740 " --> pdb=" O GLY A 770 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N CYS A 772 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A 973 " --> pdb=" O ILE A1006 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE A1008 " --> pdb=" O ILE A 973 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE A 975 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 972 " --> pdb=" O THR A 830 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 976 " --> pdb=" O TYR A 834 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS A 860 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE A 833 " --> pdb=" O LYS A 860 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG A 862 " --> pdb=" O ILE A 833 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TRP A 835 " --> pdb=" O ARG A 862 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE A 864 " --> pdb=" O TRP A 835 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 677 through 679 removed outlier: 7.058A pdb=" N VAL A 712 " --> pdb=" O LEU A 678 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 892 through 896 removed outlier: 6.798A pdb=" N LEU B 972 " --> pdb=" O ASP B 832 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TYR B 834 " --> pdb=" O LEU B 972 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL B 974 " --> pdb=" O TYR B 834 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY B 741 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE B 708 " --> pdb=" O CYS B 674 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N HIS B 676 " --> pdb=" O PHE B 708 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER B 710 " --> pdb=" O HIS B 676 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LEU B 678 " --> pdb=" O SER B 710 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 712 " --> pdb=" O LEU B 678 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1608 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: 4.29 Time building geometry restraints manager: 5.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2278 1.32 - 1.46: 4615 1.46 - 1.59: 6928 1.59 - 1.73: 15 1.73 - 1.86: 122 Bond restraints: 13958 Sorted by residual: bond pdb=" C4 ATP B1101 " pdb=" C5 ATP B1101 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C4 ATP A1101 " pdb=" C5 ATP A1101 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.69e+01 bond pdb=" C5 ATP B1101 " pdb=" C6 ATP B1101 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.09e+01 bond pdb=" N ARG A 559 " pdb=" CA ARG A 559 " ideal model delta sigma weight residual 1.462 1.396 0.065 1.06e-02 8.90e+03 3.82e+01 bond pdb=" C5 ATP A1101 " pdb=" C6 ATP A1101 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.00e-02 1.00e+04 3.77e+01 ... (remaining 13953 not shown) Histogram of bond angle deviations from ideal: 96.88 - 104.93: 260 104.93 - 112.99: 7539 112.99 - 121.04: 7439 121.04 - 129.10: 3622 129.10 - 137.15: 127 Bond angle restraints: 18987 Sorted by residual: angle pdb=" PA ATP A1101 " pdb=" O3A ATP A1101 " pdb=" PB ATP A1101 " ideal model delta sigma weight residual 136.83 114.59 22.24 1.00e+00 1.00e+00 4.95e+02 angle pdb=" PB ATP A1101 " pdb=" O3B ATP A1101 " pdb=" PG ATP A1101 " ideal model delta sigma weight residual 139.87 120.98 18.89 1.00e+00 1.00e+00 3.57e+02 angle pdb=" PB ATP B1101 " pdb=" O3B ATP B1101 " pdb=" PG ATP B1101 " ideal model delta sigma weight residual 139.87 121.94 17.93 1.00e+00 1.00e+00 3.21e+02 angle pdb=" PA ATP B1101 " pdb=" O3A ATP B1101 " pdb=" PB ATP B1101 " ideal model delta sigma weight residual 136.83 125.99 10.84 1.00e+00 1.00e+00 1.17e+02 angle pdb=" C5 ATP B1101 " pdb=" C4 ATP B1101 " pdb=" N3 ATP B1101 " ideal model delta sigma weight residual 126.80 118.38 8.42 1.00e+00 1.00e+00 7.10e+01 ... (remaining 18982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 7341 17.78 - 35.56: 647 35.56 - 53.34: 121 53.34 - 71.12: 27 71.12 - 88.90: 13 Dihedral angle restraints: 8149 sinusoidal: 3201 harmonic: 4948 Sorted by residual: dihedral pdb=" CB CYS A 416 " pdb=" SG CYS A 416 " pdb=" SG CYS A 421 " pdb=" CB CYS A 421 " ideal model delta sinusoidal sigma weight residual -86.00 -170.69 84.69 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 436 " pdb=" CB CYS A 436 " ideal model delta sinusoidal sigma weight residual 93.00 16.62 76.38 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CB CYS B 416 " pdb=" SG CYS B 416 " pdb=" SG CYS B 421 " pdb=" CB CYS B 421 " ideal model delta sinusoidal sigma weight residual 93.00 29.23 63.77 1 1.00e+01 1.00e-02 5.36e+01 ... (remaining 8146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1553 0.056 - 0.111: 488 0.111 - 0.167: 99 0.167 - 0.222: 8 0.222 - 0.278: 3 Chirality restraints: 2151 Sorted by residual: chirality pdb=" CA PHE B 495 " pdb=" N PHE B 495 " pdb=" C PHE B 495 " pdb=" CB PHE B 495 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ALA B 916 " pdb=" N ALA B 916 " pdb=" C ALA B 916 " pdb=" CB ALA B 916 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA TRP A 612 " pdb=" N TRP A 612 " pdb=" C TRP A 612 " pdb=" CB TRP A 612 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 2148 not shown) Planarity restraints: 2355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 430 " 0.021 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C CYS A 430 " -0.071 2.00e-02 2.50e+03 pdb=" O CYS A 430 " 0.027 2.00e-02 2.50e+03 pdb=" N THR A 431 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 431 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.26e+00 pdb=" C THR A 431 " -0.053 2.00e-02 2.50e+03 pdb=" O THR A 431 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN A 432 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 913 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.49e+00 pdb=" C ASP B 913 " 0.050 2.00e-02 2.50e+03 pdb=" O ASP B 913 " -0.019 2.00e-02 2.50e+03 pdb=" N MET B 914 " -0.017 2.00e-02 2.50e+03 ... (remaining 2352 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1866 2.75 - 3.28: 12980 3.28 - 3.82: 21442 3.82 - 4.36: 26467 4.36 - 4.90: 46012 Nonbonded interactions: 108767 Sorted by model distance: nonbonded pdb=" OD2 ASP A 839 " pdb=" OG1 THR A 843 " model vdw 2.207 2.440 nonbonded pdb=" OD1 ASN B1014 " pdb=" NH1 ARG C 162 " model vdw 2.224 2.520 nonbonded pdb=" O PRO A 643 " pdb=" OG SER A 670 " model vdw 2.228 2.440 nonbonded pdb=" NH2 ARG B1009 " pdb=" OD2 ASP C 141 " model vdw 2.246 2.520 nonbonded pdb=" NH2 ARG B 145 " pdb=" OE2 GLU B 282 " model vdw 2.251 2.520 ... (remaining 108762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 131 through 605 or resid 620 through 1020 or resid 1101 th \ rough 1103)) selection = (chain 'B' and (resid 131 through 866 or resid 880 through 1020 or resid 1101 th \ rough 1103)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.070 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 35.980 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.050 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:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.009 0.073 13958 Z= 0.563 Angle : 0.938 22.244 18987 Z= 0.578 Chirality : 0.054 0.278 2151 Planarity : 0.006 0.062 2355 Dihedral : 14.064 88.897 4965 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.19), residues: 1707 helix: -0.79 (0.17), residues: 924 sheet: -0.83 (0.45), residues: 139 loop : -2.14 (0.22), residues: 644 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 196 time to evaluate : 1.604 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 209 average time/residue: 1.2825 time to fit residues: 293.6566 Evaluate side-chains 168 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 1.445 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.9642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 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 901 GLN B 359 ASN B 684 GLN B 874 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 13958 Z= 0.165 Angle : 0.548 7.077 18987 Z= 0.281 Chirality : 0.041 0.161 2151 Planarity : 0.004 0.039 2355 Dihedral : 6.000 88.466 1875 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1707 helix: 0.03 (0.17), residues: 927 sheet: -0.46 (0.46), residues: 139 loop : -1.94 (0.22), residues: 641 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 189 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 16 residues processed: 207 average time/residue: 1.1638 time to fit residues: 266.1235 Evaluate side-chains 181 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.533 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 5 residues processed: 11 average time/residue: 0.3312 time to fit residues: 7.0493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 128 optimal weight: 0.2980 chunk 105 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN B 684 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 13958 Z= 0.185 Angle : 0.515 7.463 18987 Z= 0.263 Chirality : 0.041 0.138 2151 Planarity : 0.003 0.033 2355 Dihedral : 5.785 87.672 1875 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.20), residues: 1707 helix: 0.41 (0.18), residues: 924 sheet: -0.23 (0.46), residues: 139 loop : -1.85 (0.22), residues: 644 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 1.567 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 17 residues processed: 182 average time/residue: 1.2127 time to fit residues: 243.7400 Evaluate side-chains 174 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 7 residues processed: 10 average time/residue: 0.5457 time to fit residues: 8.6757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 80 optimal weight: 0.0060 chunk 17 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN A 901 GLN B 359 ASN B 644 GLN B 900 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 13958 Z= 0.348 Angle : 0.590 8.364 18987 Z= 0.298 Chirality : 0.045 0.154 2151 Planarity : 0.004 0.040 2355 Dihedral : 5.882 88.283 1875 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.20), residues: 1707 helix: 0.34 (0.18), residues: 922 sheet: -0.28 (0.45), residues: 139 loop : -1.78 (0.22), residues: 646 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 167 time to evaluate : 1.577 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 25 residues processed: 189 average time/residue: 1.2028 time to fit residues: 253.3012 Evaluate side-chains 187 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 1.629 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 13 residues processed: 12 average time/residue: 0.2614 time to fit residues: 6.8549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 0.0870 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 434 HIS A 750 HIS A 901 GLN B 359 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 13958 Z= 0.166 Angle : 0.493 8.316 18987 Z= 0.252 Chirality : 0.040 0.149 2151 Planarity : 0.003 0.041 2355 Dihedral : 5.589 88.473 1875 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.20), residues: 1707 helix: 0.64 (0.18), residues: 922 sheet: -0.09 (0.45), residues: 139 loop : -1.67 (0.22), residues: 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 164 time to evaluate : 1.528 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 21 residues processed: 190 average time/residue: 1.1413 time to fit residues: 240.3735 Evaluate side-chains 177 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 1.538 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 12 residues processed: 10 average time/residue: 0.4510 time to fit residues: 7.7678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 644 GLN B 745 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 13958 Z= 0.390 Angle : 0.610 8.716 18987 Z= 0.308 Chirality : 0.046 0.169 2151 Planarity : 0.004 0.051 2355 Dihedral : 5.801 89.092 1875 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1707 helix: 0.38 (0.18), residues: 926 sheet: -0.18 (0.45), residues: 139 loop : -1.76 (0.22), residues: 642 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 169 time to evaluate : 1.428 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 26 residues processed: 197 average time/residue: 1.1372 time to fit residues: 248.8814 Evaluate side-chains 189 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 15 residues processed: 11 average time/residue: 0.3332 time to fit residues: 7.0484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 0.0170 chunk 138 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 HIS B 644 GLN B 745 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 13958 Z= 0.192 Angle : 0.508 8.752 18987 Z= 0.258 Chirality : 0.041 0.155 2151 Planarity : 0.004 0.048 2355 Dihedral : 5.561 89.168 1875 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 2.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.20), residues: 1707 helix: 0.68 (0.18), residues: 922 sheet: -0.11 (0.44), residues: 141 loop : -1.67 (0.22), residues: 644 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 162 time to evaluate : 1.690 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 26 residues processed: 190 average time/residue: 1.0588 time to fit residues: 225.1144 Evaluate side-chains 183 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 1.721 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 8 average time/residue: 0.7661 time to fit residues: 9.1548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN B 745 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 13958 Z= 0.164 Angle : 0.492 9.136 18987 Z= 0.250 Chirality : 0.040 0.154 2151 Planarity : 0.004 0.052 2355 Dihedral : 5.365 89.211 1875 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1707 helix: 0.92 (0.18), residues: 919 sheet: 0.04 (0.45), residues: 141 loop : -1.58 (0.22), residues: 647 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 152 time to evaluate : 1.384 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 24 residues processed: 177 average time/residue: 1.0336 time to fit residues: 205.6308 Evaluate side-chains 170 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 1.566 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 7 average time/residue: 0.2038 time to fit residues: 4.4288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 745 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 13958 Z= 0.277 Angle : 0.552 9.320 18987 Z= 0.278 Chirality : 0.043 0.161 2151 Planarity : 0.004 0.059 2355 Dihedral : 5.477 89.593 1875 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.20), residues: 1707 helix: 0.75 (0.18), residues: 925 sheet: -0.02 (0.44), residues: 141 loop : -1.59 (0.22), residues: 641 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.574 Fit side-chains outliers start: 29 outliers final: 26 residues processed: 186 average time/residue: 1.0264 time to fit residues: 214.9341 Evaluate side-chains 189 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 17 residues processed: 10 average time/residue: 0.3040 time to fit residues: 6.5000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 112 optimal weight: 0.0670 chunk 169 optimal weight: 0.0980 chunk 155 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.0324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 ASN A 750 HIS B 745 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 13958 Z= 0.180 Angle : 0.505 9.405 18987 Z= 0.256 Chirality : 0.041 0.151 2151 Planarity : 0.004 0.060 2355 Dihedral : 5.336 89.620 1875 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 1707 helix: 0.96 (0.18), residues: 919 sheet: 0.09 (0.44), residues: 141 loop : -1.55 (0.22), residues: 647 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 1.545 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 18 residues processed: 165 average time/residue: 1.0742 time to fit residues: 198.4372 Evaluate side-chains 164 residues out of total 1453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 2 average time/residue: 0.2775 time to fit residues: 2.9080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 19 optimal weight: 0.0070 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 118 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 644 GLN B 745 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.172483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126883 restraints weight = 15085.592| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.50 r_work: 0.3453 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 13958 Z= 0.131 Angle : 0.477 10.304 18987 Z= 0.239 Chirality : 0.039 0.145 2151 Planarity : 0.003 0.059 2355 Dihedral : 4.993 89.340 1875 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.21), residues: 1707 helix: 1.29 (0.18), residues: 924 sheet: 0.29 (0.45), residues: 141 loop : -1.44 (0.22), residues: 642 =============================================================================== Job complete usr+sys time: 4594.83 seconds wall clock time: 82 minutes 41.79 seconds (4961.79 seconds total)