Starting phenix.real_space_refine on Fri Jan 19 10:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iab_35299/01_2024/8iab_35299_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iab_35299/01_2024/8iab_35299.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iab_35299/01_2024/8iab_35299_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iab_35299/01_2024/8iab_35299_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iab_35299/01_2024/8iab_35299_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iab_35299/01_2024/8iab_35299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iab_35299/01_2024/8iab_35299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iab_35299/01_2024/8iab_35299_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iab_35299/01_2024/8iab_35299_updated.pdb" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 Mg 2 5.21 5 S 58 5.16 5 Cl 6 4.86 5 C 7192 2.51 5 N 1836 2.21 5 O 1988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 505": "OD1" <-> "OD2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 577": "OE1" <-> "OE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 767": "OD1" <-> "OD2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 505": "OD1" <-> "OD2" Residue "B GLU 534": "OE1" <-> "OE2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 577": "OE1" <-> "OE2" Residue "B GLU 606": "OE1" <-> "OE2" Residue "B ARG 616": "NH1" <-> "NH2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 692": "OE1" <-> "OE2" Residue "B TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 767": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 11094 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5465 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 28, 'TRANS': 675} Chain breaks: 2 Chain: "B" Number of atoms: 5465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5465 Classifications: {'peptide': 704} Link IDs: {'PTRANS': 28, 'TRANS': 675} Chain breaks: 2 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 82 Unusual residues: {' CL': 3, ' MG': 1, 'ATP': 1, 'PIO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 82 Unusual residues: {' CL': 3, ' MG': 1, 'ATP': 1, 'PIO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 6.46, per 1000 atoms: 0.58 Number of scatterers: 11094 At special positions: 0 Unit cell: (110.39, 87.15, 107.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 6 17.00 S 58 16.00 P 12 15.00 Mg 2 11.99 O 1988 8.00 N 1836 7.00 C 7192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 419 " distance=2.04 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 419 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.45 Conformation dependent library (CDL) restraints added in 2.2 seconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 10 sheets defined 59.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 76 through 123 removed outlier: 3.564A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 109 " --> pdb=" O ASN A 105 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 153 removed outlier: 3.533A pdb=" N VAL A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 180 through 194 removed outlier: 3.542A pdb=" N ALA A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 219 removed outlier: 3.813A pdb=" N VAL A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.877A pdb=" N TYR A 234 " --> pdb=" O TRP A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 257 removed outlier: 3.595A pdb=" N ASP A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 removed outlier: 4.018A pdb=" N VAL A 264 " --> pdb=" O PRO A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 301 removed outlier: 3.512A pdb=" N VAL A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 365 removed outlier: 3.794A pdb=" N ILE A 331 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A 332 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 3.616A pdb=" N VAL A 339 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 340 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 341 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 343 " --> pdb=" O PHE A 340 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU A 344 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY A 345 " --> pdb=" O GLY A 342 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 347 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR A 348 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 351 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 352 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS A 353 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A 356 " --> pdb=" O HIS A 353 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 359 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A 360 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 363 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 364 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.578A pdb=" N VAL A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 388 " --> pdb=" O CYS A 384 " (cutoff:3.500A) Proline residue: A 389 - end of helix Processing helix chain 'A' and resid 428 through 431 No H-bonds generated for 'chain 'A' and resid 428 through 431' Processing helix chain 'A' and resid 435 through 442 removed outlier: 3.739A pdb=" N ARG A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 470 removed outlier: 3.524A pdb=" N ILE A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 468 " --> pdb=" O CYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 498 removed outlier: 3.788A pdb=" N TYR A 490 " --> pdb=" O MET A 486 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.600A pdb=" N VAL A 530 " --> pdb=" O VAL A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 558 removed outlier: 3.713A pdb=" N LEU A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Proline residue: A 543 - end of helix removed outlier: 3.783A pdb=" N MET A 546 " --> pdb=" O PRO A 543 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 547 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 549 " --> pdb=" O MET A 546 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 551 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 552 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS A 553 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 555 " --> pdb=" O ALA A 552 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 556 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 557 " --> pdb=" O THR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 570 Processing helix chain 'A' and resid 582 through 586 removed outlier: 3.656A pdb=" N ARG A 585 " --> pdb=" O PRO A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 595 removed outlier: 3.679A pdb=" N ASP A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 616 Processing helix chain 'A' and resid 643 through 652 removed outlier: 3.734A pdb=" N LYS A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 670 removed outlier: 4.105A pdb=" N ARG A 668 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 669 " --> pdb=" O TRP A 665 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 664 through 670' Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.598A pdb=" N ALA A 677 " --> pdb=" O PRO A 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 673 through 677' Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 716 through 726 Processing helix chain 'A' and resid 756 through 762 removed outlier: 4.090A pdb=" N GLN A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 762 " --> pdb=" O ASN A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 766 No H-bonds generated for 'chain 'A' and resid 764 through 766' Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 76 through 123 removed outlier: 3.564A pdb=" N PHE B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 153 removed outlier: 3.533A pdb=" N VAL B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 180 through 194 removed outlier: 3.542A pdb=" N ALA B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 219 removed outlier: 3.813A pdb=" N VAL B 207 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 3.877A pdb=" N TYR B 234 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 257 removed outlier: 3.595A pdb=" N ASP B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 removed outlier: 4.018A pdb=" N VAL B 264 " --> pdb=" O PRO B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 301 removed outlier: 3.512A pdb=" N VAL B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 365 removed outlier: 3.794A pdb=" N ILE B 331 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE B 332 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 3.616A pdb=" N VAL B 339 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 340 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 341 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE B 343 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU B 344 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY B 345 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR B 348 " --> pdb=" O GLY B 345 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 351 " --> pdb=" O TYR B 348 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B 352 " --> pdb=" O ASN B 349 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS B 353 " --> pdb=" O HIS B 350 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU B 356 " --> pdb=" O HIS B 353 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 359 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN B 360 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN B 363 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 364 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 391 removed outlier: 3.578A pdb=" N VAL B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 388 " --> pdb=" O CYS B 384 " (cutoff:3.500A) Proline residue: B 389 - end of helix Processing helix chain 'B' and resid 428 through 431 No H-bonds generated for 'chain 'B' and resid 428 through 431' Processing helix chain 'B' and resid 435 through 442 removed outlier: 3.739A pdb=" N ARG B 440 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 470 removed outlier: 3.524A pdb=" N ILE B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 468 " --> pdb=" O CYS B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 498 removed outlier: 3.788A pdb=" N TYR B 490 " --> pdb=" O MET B 486 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 521 Processing helix chain 'B' and resid 526 through 535 removed outlier: 3.600A pdb=" N VAL B 530 " --> pdb=" O VAL B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 558 removed outlier: 3.713A pdb=" N LEU B 542 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Proline residue: B 543 - end of helix removed outlier: 3.783A pdb=" N MET B 546 " --> pdb=" O PRO B 543 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B 547 " --> pdb=" O ILE B 544 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 549 " --> pdb=" O MET B 546 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 551 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 552 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS B 553 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL B 555 " --> pdb=" O ALA B 552 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 556 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP B 557 " --> pdb=" O THR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 570 Processing helix chain 'B' and resid 582 through 586 removed outlier: 3.656A pdb=" N ARG B 585 " --> pdb=" O PRO B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 595 removed outlier: 3.679A pdb=" N ASP B 594 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 616 Processing helix chain 'B' and resid 643 through 652 removed outlier: 3.734A pdb=" N LYS B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 670 removed outlier: 4.105A pdb=" N ARG B 668 " --> pdb=" O GLU B 664 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 669 " --> pdb=" O TRP B 665 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 664 through 670' Processing helix chain 'B' and resid 673 through 677 removed outlier: 3.598A pdb=" N ALA B 677 " --> pdb=" O PRO B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 677' Processing helix chain 'B' and resid 683 through 685 No H-bonds generated for 'chain 'B' and resid 683 through 685' Processing helix chain 'B' and resid 700 through 702 No H-bonds generated for 'chain 'B' and resid 700 through 702' Processing helix chain 'B' and resid 716 through 726 Processing helix chain 'B' and resid 756 through 762 removed outlier: 4.090A pdb=" N GLN B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 762 " --> pdb=" O ASN B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 766 No H-bonds generated for 'chain 'B' and resid 764 through 766' Processing sheet with id= A, first strand: chain 'A' and resid 44 through 47 Processing sheet with id= B, first strand: chain 'A' and resid 394 through 396 Processing sheet with id= C, first strand: chain 'A' and resid 601 through 603 removed outlier: 8.038A pdb=" N LEU A 602 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 639 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 605 through 607 Processing sheet with id= E, first strand: chain 'A' and resid 709 through 711 removed outlier: 6.459A pdb=" N LEU A 732 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 747 " --> pdb=" O VAL A 733 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 44 through 47 Processing sheet with id= G, first strand: chain 'B' and resid 394 through 396 Processing sheet with id= H, first strand: chain 'B' and resid 601 through 603 removed outlier: 8.038A pdb=" N LEU B 602 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 639 " --> pdb=" O VAL B 625 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 605 through 607 Processing sheet with id= J, first strand: chain 'B' and resid 709 through 711 removed outlier: 6.459A pdb=" N LEU B 732 " --> pdb=" O VAL B 710 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY B 747 " --> pdb=" O VAL B 733 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.25 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1724 1.30 - 1.43: 2944 1.43 - 1.56: 6560 1.56 - 1.68: 18 1.68 - 1.81: 92 Bond restraints: 11338 Sorted by residual: bond pdb=" C4 ATP B 800 " pdb=" C5 ATP B 800 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" C4 ATP A 800 " pdb=" C5 ATP A 800 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" C5 ATP A 800 " pdb=" C6 ATP A 800 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.90e+01 bond pdb=" C5 ATP B 800 " pdb=" C6 ATP B 800 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.90e+01 bond pdb=" C4 ATP B 800 " pdb=" N9 ATP B 800 " ideal model delta sigma weight residual 1.374 1.328 0.046 1.00e-02 1.00e+04 2.08e+01 ... (remaining 11333 not shown) Histogram of bond angle deviations from ideal: 98.36 - 106.00: 256 106.00 - 113.64: 6500 113.64 - 121.28: 5910 121.28 - 128.92: 2674 128.92 - 136.56: 98 Bond angle restraints: 15438 Sorted by residual: angle pdb=" PB ATP B 800 " pdb=" O3B ATP B 800 " pdb=" PG ATP B 800 " ideal model delta sigma weight residual 139.87 123.46 16.41 1.00e+00 1.00e+00 2.69e+02 angle pdb=" PB ATP A 800 " pdb=" O3B ATP A 800 " pdb=" PG ATP A 800 " ideal model delta sigma weight residual 139.87 123.46 16.41 1.00e+00 1.00e+00 2.69e+02 angle pdb=" PA ATP B 800 " pdb=" O3A ATP B 800 " pdb=" PB ATP B 800 " ideal model delta sigma weight residual 136.83 123.66 13.17 1.00e+00 1.00e+00 1.73e+02 angle pdb=" PA ATP A 800 " pdb=" O3A ATP A 800 " pdb=" PB ATP A 800 " ideal model delta sigma weight residual 136.83 123.66 13.17 1.00e+00 1.00e+00 1.73e+02 angle pdb=" C5 ATP B 800 " pdb=" C4 ATP B 800 " pdb=" N3 ATP B 800 " ideal model delta sigma weight residual 126.80 119.15 7.65 1.00e+00 1.00e+00 5.86e+01 ... (remaining 15433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 6072 17.68 - 35.37: 472 35.37 - 53.05: 92 53.05 - 70.73: 28 70.73 - 88.42: 10 Dihedral angle restraints: 6674 sinusoidal: 2654 harmonic: 4020 Sorted by residual: dihedral pdb=" CB CYS A 394 " pdb=" SG CYS A 394 " pdb=" SG CYS A 419 " pdb=" CB CYS A 419 " ideal model delta sinusoidal sigma weight residual -86.00 -121.10 35.10 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CB CYS B 394 " pdb=" SG CYS B 394 " pdb=" SG CYS B 419 " pdb=" CB CYS B 419 " ideal model delta sinusoidal sigma weight residual -86.00 -121.10 35.10 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CA TYR B 463 " pdb=" C TYR B 463 " pdb=" N CYS B 464 " pdb=" CA CYS B 464 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 6671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1116 0.039 - 0.077: 544 0.077 - 0.116: 118 0.116 - 0.155: 34 0.155 - 0.193: 2 Chirality restraints: 1814 Sorted by residual: chirality pdb=" CA GLU A 323 " pdb=" N GLU A 323 " pdb=" C GLU A 323 " pdb=" CB GLU A 323 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA GLU B 323 " pdb=" N GLU B 323 " pdb=" C GLU B 323 " pdb=" CB GLU B 323 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA LEU A 388 " pdb=" N LEU A 388 " pdb=" C LEU A 388 " pdb=" CB LEU A 388 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 1811 not shown) Planarity restraints: 1902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 388 " 0.044 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO B 389 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 389 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 389 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 388 " -0.044 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO A 389 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 481 " 0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 482 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 482 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 482 " 0.032 5.00e-02 4.00e+02 ... (remaining 1899 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 23 2.41 - 3.03: 5351 3.03 - 3.65: 16487 3.65 - 4.28: 26720 4.28 - 4.90: 43625 Nonbonded interactions: 92206 Sorted by model distance: nonbonded pdb=" OE2 GLU A 55 " pdb="MG MG A 801 " model vdw 1.783 2.170 nonbonded pdb=" O1B ATP A 800 " pdb="MG MG A 801 " model vdw 2.023 2.170 nonbonded pdb=" OH TYR A 564 " pdb="CL CL A 804 " model vdw 2.023 2.590 nonbonded pdb=" OH TYR B 564 " pdb="CL CL B 804 " model vdw 2.024 2.590 nonbonded pdb=" OE2 GLU B 55 " pdb="MG MG B 801 " model vdw 2.102 2.170 ... (remaining 92201 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' selection = chain 'B' } 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: 0.980 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: 5.910 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 32.800 Find NCS groups from input model: 0.550 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: 0.000 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 11338 Z= 0.315 Angle : 0.846 16.413 15438 Z= 0.520 Chirality : 0.046 0.193 1814 Planarity : 0.006 0.065 1902 Dihedral : 13.948 88.417 4086 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: -5.05 (0.15), residues: 1396 helix: -4.13 (0.07), residues: 814 sheet: -1.86 (1.22), residues: 20 loop : -1.82 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 274 HIS 0.002 0.001 HIS A 321 PHE 0.010 0.001 PHE A 683 TYR 0.013 0.001 TYR B 490 ARG 0.004 0.000 ARG B 523 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.7485 (t80) cc_final: 0.7169 (t80) REVERT: A 123 ILE cc_start: 0.8444 (pt) cc_final: 0.8162 (mt) REVERT: A 367 LYS cc_start: 0.8563 (mttt) cc_final: 0.8283 (mtmt) REVERT: A 577 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7232 (mm-30) REVERT: A 678 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 753 ASP cc_start: 0.8627 (m-30) cc_final: 0.8408 (m-30) REVERT: A 757 TYR cc_start: 0.7339 (t80) cc_final: 0.7011 (t80) REVERT: B 121 TYR cc_start: 0.7483 (t80) cc_final: 0.7165 (t80) REVERT: B 123 ILE cc_start: 0.8437 (pt) cc_final: 0.8158 (mt) REVERT: B 367 LYS cc_start: 0.8561 (mttt) cc_final: 0.8283 (mtmt) REVERT: B 577 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7231 (mm-30) REVERT: B 678 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7715 (mt-10) REVERT: B 753 ASP cc_start: 0.8622 (m-30) cc_final: 0.8408 (m-30) REVERT: B 757 TYR cc_start: 0.7342 (t80) cc_final: 0.7016 (t80) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 1.5238 time to fit residues: 289.0939 Evaluate side-chains 126 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 657 ASN A 758 ASN B 237 ASN B 657 ASN B 758 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 11338 Z= 0.297 Angle : 0.600 7.786 15438 Z= 0.307 Chirality : 0.043 0.314 1814 Planarity : 0.006 0.048 1902 Dihedral : 10.128 86.933 1626 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.19 % Allowed : 8.77 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.76 (0.20), residues: 1396 helix: -1.05 (0.16), residues: 780 sheet: -1.10 (1.31), residues: 20 loop : -1.13 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 87 HIS 0.003 0.001 HIS B 353 PHE 0.015 0.002 PHE B 284 TYR 0.017 0.001 TYR A 463 ARG 0.007 0.001 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ILE cc_start: 0.8036 (pt) cc_final: 0.7794 (mm) REVERT: A 177 MET cc_start: 0.8618 (tpt) cc_final: 0.8294 (tpt) REVERT: A 367 LYS cc_start: 0.8377 (mttt) cc_final: 0.8155 (mtmt) REVERT: A 565 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: A 577 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7252 (mm-30) REVERT: A 678 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7691 (mt-10) REVERT: A 757 TYR cc_start: 0.7318 (t80) cc_final: 0.7086 (t80) REVERT: A 761 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.6901 (mm-40) REVERT: B 123 ILE cc_start: 0.8032 (pt) cc_final: 0.7790 (mm) REVERT: B 177 MET cc_start: 0.8621 (tpt) cc_final: 0.8300 (tpt) REVERT: B 367 LYS cc_start: 0.8377 (mttt) cc_final: 0.8155 (mtmt) REVERT: B 565 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7280 (mt-10) REVERT: B 577 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7250 (mm-30) REVERT: B 678 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7693 (mt-10) REVERT: B 757 TYR cc_start: 0.7319 (t80) cc_final: 0.7086 (t80) REVERT: B 761 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.6901 (mm-40) outliers start: 26 outliers final: 8 residues processed: 144 average time/residue: 1.5258 time to fit residues: 235.1214 Evaluate side-chains 144 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 761 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 761 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 105 optimal weight: 0.0070 chunk 86 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 127 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN B 237 ASN B 657 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11338 Z= 0.196 Angle : 0.514 6.857 15438 Z= 0.262 Chirality : 0.041 0.209 1814 Planarity : 0.004 0.045 1902 Dihedral : 9.499 80.370 1626 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.69 % Allowed : 11.97 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.45 (0.21), residues: 1396 helix: 0.26 (0.18), residues: 778 sheet: -0.68 (1.25), residues: 20 loop : -0.95 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 87 HIS 0.002 0.000 HIS A 353 PHE 0.011 0.001 PHE B 135 TYR 0.014 0.001 TYR B 463 ARG 0.006 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 1.204 Fit side-chains REVERT: A 76 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8343 (tptt) REVERT: A 367 LYS cc_start: 0.8287 (mttt) cc_final: 0.8043 (mtmt) REVERT: A 486 MET cc_start: 0.8338 (ttm) cc_final: 0.8052 (mtp) REVERT: A 577 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7237 (mm-30) REVERT: A 659 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8478 (mttp) REVERT: A 678 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7678 (mt-10) REVERT: A 757 TYR cc_start: 0.7321 (t80) cc_final: 0.7092 (t80) REVERT: B 76 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8342 (tptt) REVERT: B 367 LYS cc_start: 0.8290 (mttt) cc_final: 0.8045 (mtmt) REVERT: B 486 MET cc_start: 0.8338 (ttm) cc_final: 0.8052 (mtp) REVERT: B 577 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7235 (mm-30) REVERT: B 659 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8478 (mttp) REVERT: B 678 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 757 TYR cc_start: 0.7320 (t80) cc_final: 0.7092 (t80) outliers start: 20 outliers final: 10 residues processed: 144 average time/residue: 1.3622 time to fit residues: 210.9290 Evaluate side-chains 136 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 635 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 3.9990 chunk 95 optimal weight: 0.0370 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.0010 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.9868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 321 HIS B 321 HIS B 657 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11338 Z= 0.186 Angle : 0.497 6.624 15438 Z= 0.253 Chirality : 0.040 0.177 1814 Planarity : 0.004 0.044 1902 Dihedral : 9.287 76.439 1626 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.36 % Allowed : 12.23 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.19 (0.22), residues: 1396 helix: 0.89 (0.19), residues: 776 sheet: -0.52 (1.25), residues: 20 loop : -0.81 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 87 HIS 0.002 0.000 HIS B 353 PHE 0.010 0.001 PHE A 135 TYR 0.015 0.001 TYR A 463 ARG 0.004 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.213 Fit side-chains REVERT: A 76 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8326 (tptt) REVERT: A 223 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7022 (t70) REVERT: A 228 LYS cc_start: 0.8328 (mmtt) cc_final: 0.8003 (tppt) REVERT: A 367 LYS cc_start: 0.8304 (mttt) cc_final: 0.8076 (mtmt) REVERT: A 486 MET cc_start: 0.8332 (ttm) cc_final: 0.8074 (mtp) REVERT: A 577 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 659 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8463 (mttp) REVERT: A 678 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7666 (mt-10) REVERT: A 757 TYR cc_start: 0.7345 (t80) cc_final: 0.7133 (t80) REVERT: B 76 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8326 (tptt) REVERT: B 223 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7027 (t70) REVERT: B 228 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8006 (tppt) REVERT: B 367 LYS cc_start: 0.8306 (mttt) cc_final: 0.8079 (mtmt) REVERT: B 486 MET cc_start: 0.8330 (ttm) cc_final: 0.8074 (mtp) REVERT: B 577 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7250 (mm-30) REVERT: B 659 LYS cc_start: 0.8678 (mtpt) cc_final: 0.8461 (mttp) REVERT: B 678 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7670 (mt-10) REVERT: B 757 TYR cc_start: 0.7344 (t80) cc_final: 0.7132 (t80) outliers start: 28 outliers final: 12 residues processed: 147 average time/residue: 1.2289 time to fit residues: 195.6468 Evaluate side-chains 141 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 546 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 121 optimal weight: 0.0570 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11338 Z= 0.386 Angle : 0.597 7.009 15438 Z= 0.301 Chirality : 0.046 0.187 1814 Planarity : 0.004 0.046 1902 Dihedral : 10.031 87.385 1626 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.53 % Allowed : 12.98 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.15 (0.22), residues: 1396 helix: 0.84 (0.19), residues: 782 sheet: -0.37 (1.02), residues: 30 loop : -0.84 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 87 HIS 0.004 0.001 HIS A 353 PHE 0.011 0.002 PHE A 723 TYR 0.023 0.002 TYR A 463 ARG 0.003 0.001 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8351 (tptt) REVERT: A 223 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7061 (t70) REVERT: A 305 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.6752 (mtpt) REVERT: A 316 MET cc_start: 0.7274 (mmm) cc_final: 0.7061 (tpp) REVERT: A 367 LYS cc_start: 0.8373 (mttt) cc_final: 0.8130 (mtmt) REVERT: A 565 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: A 577 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7251 (mm-30) REVERT: A 659 LYS cc_start: 0.8682 (mtpt) cc_final: 0.8437 (mttp) REVERT: A 678 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7737 (mt-10) REVERT: A 757 TYR cc_start: 0.7359 (t80) cc_final: 0.7111 (t80) REVERT: B 76 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8349 (tptt) REVERT: B 223 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7069 (t70) REVERT: B 305 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.6751 (mtpt) REVERT: B 316 MET cc_start: 0.7280 (mmm) cc_final: 0.7066 (tpp) REVERT: B 367 LYS cc_start: 0.8374 (mttt) cc_final: 0.8132 (mtmt) REVERT: B 565 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: B 577 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7248 (mm-30) REVERT: B 659 LYS cc_start: 0.8685 (mtpt) cc_final: 0.8441 (mttp) REVERT: B 678 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7739 (mt-10) REVERT: B 757 TYR cc_start: 0.7357 (t80) cc_final: 0.7111 (t80) outliers start: 30 outliers final: 18 residues processed: 141 average time/residue: 1.4645 time to fit residues: 222.4625 Evaluate side-chains 152 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 691 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 11 optimal weight: 0.0870 chunk 44 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 130 optimal weight: 0.4980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 657 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11338 Z= 0.137 Angle : 0.469 5.689 15438 Z= 0.241 Chirality : 0.039 0.165 1814 Planarity : 0.004 0.044 1902 Dihedral : 9.223 85.314 1626 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.69 % Allowed : 13.83 % Favored : 84.49 % 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: 0.65 (0.22), residues: 1396 helix: 1.36 (0.19), residues: 778 sheet: -0.41 (1.19), residues: 20 loop : -0.77 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 87 HIS 0.001 0.000 HIS B 730 PHE 0.009 0.001 PHE B 723 TYR 0.012 0.001 TYR B 463 ARG 0.004 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8316 (tptt) REVERT: A 223 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7163 (m-30) REVERT: A 228 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7878 (tppt) REVERT: A 305 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6571 (mtpt) REVERT: A 367 LYS cc_start: 0.8311 (mttt) cc_final: 0.8068 (mtmt) REVERT: A 486 MET cc_start: 0.8220 (ttm) cc_final: 0.7984 (mtp) REVERT: A 577 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7242 (mm-30) REVERT: A 659 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8469 (mttp) REVERT: A 678 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7649 (mt-10) REVERT: A 757 TYR cc_start: 0.7326 (t80) cc_final: 0.7108 (t80) REVERT: B 76 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8314 (tptt) REVERT: B 223 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.6977 (t70) REVERT: B 228 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7885 (tppt) REVERT: B 305 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6568 (mtpt) REVERT: B 367 LYS cc_start: 0.8311 (mttt) cc_final: 0.8070 (mtmt) REVERT: B 486 MET cc_start: 0.8220 (ttm) cc_final: 0.7983 (mtp) REVERT: B 577 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7237 (mm-30) REVERT: B 659 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8466 (mttp) REVERT: B 678 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7651 (mt-10) REVERT: B 757 TYR cc_start: 0.7326 (t80) cc_final: 0.7108 (t80) outliers start: 20 outliers final: 8 residues processed: 133 average time/residue: 1.4327 time to fit residues: 204.5974 Evaluate side-chains 137 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 691 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 98 optimal weight: 0.0070 chunk 76 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 ASN B 657 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11338 Z= 0.144 Angle : 0.462 5.364 15438 Z= 0.237 Chirality : 0.039 0.153 1814 Planarity : 0.003 0.044 1902 Dihedral : 8.821 81.162 1626 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.85 % Allowed : 14.25 % Favored : 83.90 % 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: 0.92 (0.23), residues: 1396 helix: 1.64 (0.19), residues: 774 sheet: -0.17 (1.19), residues: 20 loop : -0.73 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 87 HIS 0.001 0.000 HIS A 730 PHE 0.010 0.001 PHE B 135 TYR 0.012 0.001 TYR B 463 ARG 0.002 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7021 (t70) REVERT: A 228 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7848 (tppt) REVERT: A 305 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6306 (mtpt) REVERT: A 367 LYS cc_start: 0.8283 (mttt) cc_final: 0.8039 (mtmt) REVERT: A 486 MET cc_start: 0.8194 (ttm) cc_final: 0.7978 (mtp) REVERT: A 659 LYS cc_start: 0.8674 (mtpt) cc_final: 0.8471 (mttp) REVERT: A 678 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7649 (mt-10) REVERT: B 223 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7026 (t70) REVERT: B 228 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7850 (tppt) REVERT: B 305 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6305 (mtpt) REVERT: B 367 LYS cc_start: 0.8292 (mttt) cc_final: 0.8043 (mtmt) REVERT: B 486 MET cc_start: 0.8192 (ttm) cc_final: 0.7975 (mtp) REVERT: B 659 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8475 (mttp) REVERT: B 678 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7650 (mt-10) outliers start: 22 outliers final: 12 residues processed: 143 average time/residue: 1.3229 time to fit residues: 203.7708 Evaluate side-chains 141 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 635 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 593 ASN B 657 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11338 Z= 0.362 Angle : 0.591 7.183 15438 Z= 0.297 Chirality : 0.045 0.174 1814 Planarity : 0.004 0.045 1902 Dihedral : 9.821 89.765 1626 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.78 % Allowed : 13.49 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.58 (0.22), residues: 1396 helix: 1.28 (0.18), residues: 780 sheet: -0.84 (0.84), residues: 40 loop : -0.72 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 87 HIS 0.003 0.001 HIS B 353 PHE 0.011 0.002 PHE A 532 TYR 0.024 0.002 TYR A 463 ARG 0.003 0.001 ARG B 724 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7104 (t70) REVERT: A 305 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.6875 (mtpt) REVERT: A 367 LYS cc_start: 0.8389 (mttt) cc_final: 0.8135 (mtmt) REVERT: A 577 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7289 (mm-30) REVERT: A 659 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8417 (mttp) REVERT: A 678 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7722 (mt-10) REVERT: B 223 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7107 (t70) REVERT: B 305 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.6845 (mtpt) REVERT: B 367 LYS cc_start: 0.8403 (mttt) cc_final: 0.8136 (mtmt) REVERT: B 577 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7286 (mm-30) REVERT: B 659 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8424 (mttp) REVERT: B 678 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7725 (mt-10) REVERT: B 753 ASP cc_start: 0.8675 (m-30) cc_final: 0.8471 (m-30) outliers start: 33 outliers final: 16 residues processed: 148 average time/residue: 1.2744 time to fit residues: 203.5038 Evaluate side-chains 151 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 635 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 712 GLN B 657 ASN B 712 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11338 Z= 0.216 Angle : 0.516 6.055 15438 Z= 0.261 Chirality : 0.041 0.168 1814 Planarity : 0.004 0.045 1902 Dihedral : 9.456 89.821 1626 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.02 % Allowed : 14.17 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.80 (0.22), residues: 1396 helix: 1.49 (0.19), residues: 780 sheet: -0.82 (0.83), residues: 40 loop : -0.67 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 87 HIS 0.002 0.000 HIS B 208 PHE 0.010 0.001 PHE A 723 TYR 0.016 0.001 TYR B 463 ARG 0.002 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7100 (t70) REVERT: A 228 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7869 (tppt) REVERT: A 305 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6696 (mtpt) REVERT: A 367 LYS cc_start: 0.8343 (mttt) cc_final: 0.8089 (mtmt) REVERT: A 577 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 659 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8421 (mttp) REVERT: A 678 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7697 (mt-10) REVERT: B 223 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7105 (t70) REVERT: B 228 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7869 (tppt) REVERT: B 305 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6698 (mtpt) REVERT: B 367 LYS cc_start: 0.8339 (mttt) cc_final: 0.8087 (mtmt) REVERT: B 577 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7323 (mm-30) REVERT: B 659 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8425 (mttp) REVERT: B 678 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7700 (mt-10) outliers start: 24 outliers final: 14 residues processed: 142 average time/residue: 1.4471 time to fit residues: 220.8547 Evaluate side-chains 150 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 635 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 712 GLN B 657 ASN B 712 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11338 Z= 0.198 Angle : 0.503 6.238 15438 Z= 0.255 Chirality : 0.041 0.160 1814 Planarity : 0.004 0.045 1902 Dihedral : 9.263 89.000 1626 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.02 % Allowed : 14.33 % Favored : 83.64 % 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: 0.93 (0.23), residues: 1396 helix: 1.63 (0.19), residues: 780 sheet: -0.84 (0.83), residues: 40 loop : -0.66 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 87 HIS 0.002 0.000 HIS A 208 PHE 0.010 0.001 PHE A 723 TYR 0.015 0.001 TYR B 463 ARG 0.002 0.000 ARG B 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7129 (t70) REVERT: A 228 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7837 (tppt) REVERT: A 305 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6612 (mtpt) REVERT: A 367 LYS cc_start: 0.8330 (mttt) cc_final: 0.8079 (mtmt) REVERT: A 486 MET cc_start: 0.8242 (ttm) cc_final: 0.8002 (mtp) REVERT: A 577 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7339 (mm-30) REVERT: A 659 LYS cc_start: 0.8670 (mtpt) cc_final: 0.8431 (mttp) REVERT: A 678 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7705 (mt-10) REVERT: B 223 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7105 (t70) REVERT: B 228 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7839 (tppt) REVERT: B 305 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6615 (mtpt) REVERT: B 367 LYS cc_start: 0.8337 (mttt) cc_final: 0.8090 (mtmt) REVERT: B 486 MET cc_start: 0.8243 (ttm) cc_final: 0.8004 (mtp) REVERT: B 577 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7337 (mm-30) REVERT: B 659 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8430 (mttp) REVERT: B 678 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7704 (mt-10) outliers start: 24 outliers final: 12 residues processed: 141 average time/residue: 1.3676 time to fit residues: 207.3518 Evaluate side-chains 145 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 635 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 111 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 712 GLN B 657 ASN B 712 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.115777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.081876 restraints weight = 12864.607| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 1.85 r_work: 0.2549 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11338 Z= 0.248 Angle : 0.535 9.248 15438 Z= 0.269 Chirality : 0.042 0.166 1814 Planarity : 0.004 0.045 1902 Dihedral : 9.416 88.911 1626 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.19 % Allowed : 14.42 % Favored : 83.39 % 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: 0.85 (0.22), residues: 1396 helix: 1.54 (0.18), residues: 780 sheet: -0.74 (0.87), residues: 40 loop : -0.67 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 87 HIS 0.002 0.000 HIS A 353 PHE 0.010 0.001 PHE A 723 TYR 0.018 0.001 TYR B 463 ARG 0.002 0.000 ARG A 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3965.11 seconds wall clock time: 71 minutes 21.97 seconds (4281.97 seconds total)