Starting phenix.real_space_refine on Sun Jul 21 00:00:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/07_2024/8u1l_41816_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/07_2024/8u1l_41816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/07_2024/8u1l_41816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/07_2024/8u1l_41816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/07_2024/8u1l_41816_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/07_2024/8u1l_41816_neut.cif" } resolution = 3.7 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= 0.003 sd= 0.016 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 61 5.16 5 C 7959 2.51 5 N 2133 2.21 5 O 2433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B GLU 602": "OE1" <-> "OE2" Residue "C GLU 425": "OE1" <-> "OE2" Residue "C GLU 545": "OE1" <-> "OE2" Residue "C GLU 607": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12595 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5171 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 14, 'TRANS': 623} Chain breaks: 1 Chain: "B" Number of atoms: 5171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5171 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 14, 'TRANS': 623} Chain breaks: 1 Chain: "C" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1483 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain breaks: 1 Chain: "D" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 706 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.12, per 1000 atoms: 0.57 Number of scatterers: 12595 At special positions: 0 Unit cell: (134.706, 117.546, 100.386, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 61 16.00 P 7 15.00 Mg 2 11.99 O 2433 8.00 N 2133 7.00 C 7959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.73 Conformation dependent library (CDL) restraints added in 2.1 seconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2936 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 14 sheets defined 47.7% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.952A pdb=" N PHE A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 61 removed outlier: 4.081A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.630A pdb=" N LEU A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 67 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 187 through 193 removed outlier: 4.186A pdb=" N ALA A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLU A 191 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 192 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 291 through 295 Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 397 through 420 removed outlier: 3.815A pdb=" N LYS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 443 removed outlier: 6.394A pdb=" N LYS A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 453 removed outlier: 3.810A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 489 through 495 removed outlier: 3.513A pdb=" N ASN A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 505 removed outlier: 4.474A pdb=" N VAL A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 Processing helix chain 'A' and resid 545 through 571 removed outlier: 5.142A pdb=" N GLY A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 612 through 617 removed outlier: 3.630A pdb=" N MET A 616 " --> pdb=" O ASP A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 631 through 644 Processing helix chain 'A' and resid 647 through 665 Processing helix chain 'A' and resid 671 through 688 removed outlier: 3.694A pdb=" N HIS A 675 " --> pdb=" O GLU A 671 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 38 through 59 removed outlier: 3.514A pdb=" N GLU B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 68 removed outlier: 6.653A pdb=" N SER B 63 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 67 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 108 through 117 Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 187 through 193 removed outlier: 3.629A pdb=" N ALA B 190 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLU B 191 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 removed outlier: 3.598A pdb=" N ILE B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.605A pdb=" N LEU B 373 " --> pdb=" O PRO B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 419 removed outlier: 3.991A pdb=" N LYS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 443 removed outlier: 6.462A pdb=" N LYS B 434 " --> pdb=" O GLU B 430 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS B 441 " --> pdb=" O LYS B 437 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 452 removed outlier: 3.990A pdb=" N ASP B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 474 Processing helix chain 'B' and resid 489 through 495 Processing helix chain 'B' and resid 498 through 505 removed outlier: 4.345A pdb=" N VAL B 502 " --> pdb=" O PHE B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 3.922A pdb=" N GLN B 523 " --> pdb=" O TYR B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 571 removed outlier: 5.565A pdb=" N GLY B 561 " --> pdb=" O VAL B 557 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU B 562 " --> pdb=" O LYS B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 removed outlier: 3.694A pdb=" N ARG B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 644 Processing helix chain 'B' and resid 647 through 665 Processing helix chain 'B' and resid 671 through 688 removed outlier: 3.783A pdb=" N HIS B 675 " --> pdb=" O GLU B 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 441 through 462 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 526 through 544 Processing helix chain 'C' and resid 553 through 564 Processing helix chain 'C' and resid 569 through 573 Processing helix chain 'C' and resid 578 through 589 Processing helix chain 'C' and resid 598 through 612 removed outlier: 3.542A pdb=" N SER C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 48 Processing helix chain 'D' and resid 103 through 112 removed outlier: 3.642A pdb=" N LYS D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU D 109 " --> pdb=" O MET D 105 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 119 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.858A pdb=" N SER B 147 " --> pdb=" O TYR B 155 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 178 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 85 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 73 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N THR B 216 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 75 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLU B 218 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 217 " --> pdb=" O THR B 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19 removed outlier: 6.652A pdb=" N GLN A 18 " --> pdb=" O ILE B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 276 through 278 removed outlier: 3.584A pdb=" N VAL A 217 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP A 278 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 178 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 148 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 322 removed outlier: 6.803A pdb=" N VAL A 334 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 317 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 332 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N HIS A 319 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA A 330 " --> pdb=" O HIS A 319 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER A 321 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE A 328 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET A 362 " --> pdb=" O LEU A 354 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL A 356 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N PHE A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 455 through 456 Processing sheet with id=AA7, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA8, first strand: chain 'A' and resid 576 through 579 removed outlier: 6.903A pdb=" N LYS A 576 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE A 627 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 578 " --> pdb=" O ILE A 627 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 359 through 362 removed outlier: 5.226A pdb=" N PHE B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 356 " --> pdb=" O PHE B 360 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET B 362 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN B 351 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL B 380 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS B 353 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N SER B 382 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR B 355 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 316 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 359 through 362 removed outlier: 5.226A pdb=" N PHE B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 356 " --> pdb=" O PHE B 360 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET B 362 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN B 351 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL B 380 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS B 353 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N SER B 382 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR B 355 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 316 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 455 through 456 Processing sheet with id=AB3, first strand: chain 'B' and resid 510 through 512 removed outlier: 8.737A pdb=" N VAL B 510 " --> pdb=" O HIS B 481 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR B 483 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N MET B 512 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 485 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 576 through 579 removed outlier: 6.697A pdb=" N LYS B 576 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE B 627 " --> pdb=" O LYS B 576 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 578 " --> pdb=" O ILE B 627 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 426 through 428 removed outlier: 3.649A pdb=" N PHE C 475 " --> pdb=" O LYS C 483 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1647 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: 4.05 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4108 1.34 - 1.46: 2486 1.46 - 1.58: 6104 1.58 - 1.70: 10 1.70 - 1.82: 105 Bond restraints: 12813 Sorted by residual: bond pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " ideal model delta sigma weight residual 1.443 1.219 0.224 1.00e-02 1.00e+04 5.02e+02 bond pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 1.443 1.224 0.219 1.00e-02 1.00e+04 4.80e+02 bond pdb=" C4' ATP A 801 " pdb=" O4' ATP A 801 " ideal model delta sigma weight residual 1.444 1.397 0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" C3' ATP B 801 " pdb=" O3' ATP B 801 " ideal model delta sigma weight residual 1.423 1.378 0.045 1.10e-02 8.26e+03 1.66e+01 bond pdb=" C3' ATP A 801 " pdb=" O3' ATP A 801 " ideal model delta sigma weight residual 1.423 1.378 0.045 1.10e-02 8.26e+03 1.64e+01 ... (remaining 12808 not shown) Histogram of bond angle deviations from ideal: 80.41 - 95.57: 7 95.57 - 110.74: 3977 110.74 - 125.91: 13107 125.91 - 141.07: 146 141.07 - 156.24: 2 Bond angle restraints: 17239 Sorted by residual: angle pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 121.27 156.24 -34.97 1.00e+00 1.00e+00 1.22e+03 angle pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " pdb=" PA ATP A 801 " ideal model delta sigma weight residual 121.27 155.38 -34.11 1.00e+00 1.00e+00 1.16e+03 angle pdb=" C3' ATP B 801 " pdb=" C4' ATP B 801 " pdb=" C5' ATP B 801 " ideal model delta sigma weight residual 115.19 83.09 32.10 1.76e+00 3.23e-01 3.33e+02 angle pdb=" C3' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " ideal model delta sigma weight residual 115.19 85.19 30.00 1.76e+00 3.23e-01 2.91e+02 angle pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 108.83 140.57 -31.74 2.33e+00 1.85e-01 1.86e+02 ... (remaining 17234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.23: 7120 18.23 - 36.47: 633 36.47 - 54.70: 120 54.70 - 72.93: 30 72.93 - 91.17: 13 Dihedral angle restraints: 7916 sinusoidal: 3380 harmonic: 4536 Sorted by residual: dihedral pdb=" CA MET A 475 " pdb=" C MET A 475 " pdb=" N LYS A 476 " pdb=" CA LYS A 476 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA MET B 93 " pdb=" C MET B 93 " pdb=" N THR B 94 " pdb=" CA THR B 94 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA LEU C 598 " pdb=" C LEU C 598 " pdb=" N PHE C 599 " pdb=" CA PHE C 599 " ideal model delta harmonic sigma weight residual 180.00 -157.70 -22.30 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1816 0.099 - 0.198: 71 0.198 - 0.297: 4 0.297 - 0.396: 1 0.396 - 0.495: 2 Chirality restraints: 1894 Sorted by residual: chirality pdb=" C4' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O4' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.99 0.50 2.00e-01 2.50e+01 6.13e+00 chirality pdb=" C4' ATP B 801 " pdb=" C3' ATP B 801 " pdb=" C5' ATP B 801 " pdb=" O4' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.97 0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" CG LEU C 538 " pdb=" CB LEU C 538 " pdb=" CD1 LEU C 538 " pdb=" CD2 LEU C 538 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 1891 not shown) Planarity restraints: 2194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 542 " 0.089 5.00e-02 4.00e+02 1.28e-01 2.62e+01 pdb=" N PRO A 543 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 112 " 0.072 5.00e-02 4.00e+02 1.06e-01 1.80e+01 pdb=" N PRO D 113 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO D 113 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 113 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 542 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO B 543 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 543 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 543 " -0.032 5.00e-02 4.00e+02 ... (remaining 2191 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 169 2.54 - 3.13: 9989 3.13 - 3.72: 20723 3.72 - 4.31: 28318 4.31 - 4.90: 45173 Nonbonded interactions: 104372 Sorted by model distance: nonbonded pdb=" O3G ATP B 801 " pdb="MG MG B 802 " model vdw 1.947 2.170 nonbonded pdb=" O3A ATP A 801 " pdb="MG MG A 802 " model vdw 2.030 2.170 nonbonded pdb=" O1G ATP A 801 " pdb="MG MG A 802 " model vdw 2.099 2.170 nonbonded pdb=" OH TYR A 425 " pdb=" O LEU A 453 " model vdw 2.176 2.440 nonbonded pdb=" OH TYR A 372 " pdb=" OD2 ASP A 443 " model vdw 2.206 2.440 ... (remaining 104367 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 group one per residue 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: 0.930 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 35.280 Find NCS groups from input model: 0.420 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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 0.224 12813 Z= 0.322 Angle : 1.066 34.971 17239 Z= 0.636 Chirality : 0.046 0.495 1894 Planarity : 0.005 0.128 2194 Dihedral : 14.738 91.169 4980 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % 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: 0.39 (0.22), residues: 1524 helix: 0.86 (0.21), residues: 643 sheet: 0.85 (0.37), residues: 201 loop : -0.42 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 31 HIS 0.006 0.001 HIS B 314 PHE 0.013 0.001 PHE A 303 TYR 0.009 0.001 TYR B 483 ARG 0.016 0.001 ARG C 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 MET cc_start: 0.8046 (mmm) cc_final: 0.7781 (mmm) REVERT: B 475 MET cc_start: 0.4892 (mmt) cc_final: 0.4605 (mmt) REVERT: C 457 ASP cc_start: 0.9102 (t70) cc_final: 0.8640 (t0) REVERT: D 105 MET cc_start: 0.3884 (tpp) cc_final: 0.1675 (ptm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2776 time to fit residues: 42.8526 Evaluate side-chains 94 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 119 optimal weight: 40.0000 chunk 46 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 GLN C 556 GLN D 9 HIS ** D 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 12813 Z= 0.360 Angle : 0.712 11.270 17239 Z= 0.376 Chirality : 0.044 0.289 1894 Planarity : 0.005 0.073 2194 Dihedral : 8.829 82.055 1741 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 25.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.88 % Allowed : 13.11 % Favored : 84.01 % 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: 0.23 (0.22), residues: 1524 helix: 0.87 (0.20), residues: 634 sheet: 0.37 (0.38), residues: 207 loop : -0.53 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 423 HIS 0.011 0.002 HIS A 314 PHE 0.015 0.002 PHE A 303 TYR 0.023 0.002 TYR A 595 ARG 0.010 0.001 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 87 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.7974 (p) REVERT: B 193 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7657 (mm) REVERT: C 469 MET cc_start: 0.6391 (mmm) cc_final: 0.6073 (mmm) REVERT: C 542 MET cc_start: 0.6169 (mmp) cc_final: 0.5559 (mmp) REVERT: C 572 LYS cc_start: 0.9047 (tptp) cc_final: 0.8738 (tptp) outliers start: 40 outliers final: 21 residues processed: 119 average time/residue: 0.2490 time to fit residues: 43.9039 Evaluate side-chains 106 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 138 optimal weight: 0.1980 chunk 149 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12813 Z= 0.175 Angle : 0.562 8.390 17239 Z= 0.297 Chirality : 0.041 0.303 1894 Planarity : 0.004 0.074 2194 Dihedral : 8.510 89.579 1741 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.03 % Allowed : 13.11 % Favored : 83.86 % 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: 0.50 (0.22), residues: 1524 helix: 1.22 (0.21), residues: 637 sheet: 0.32 (0.38), residues: 207 loop : -0.46 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 157 HIS 0.006 0.001 HIS A 314 PHE 0.010 0.001 PHE C 559 TYR 0.016 0.001 TYR A 595 ARG 0.008 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 86 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.7883 (p) REVERT: A 125 MET cc_start: 0.8180 (mmm) cc_final: 0.7389 (mmp) REVERT: B 332 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8067 (mm) REVERT: B 622 LYS cc_start: 0.7266 (tptt) cc_final: 0.6614 (tptt) REVERT: C 469 MET cc_start: 0.6234 (mmm) cc_final: 0.5914 (mmm) REVERT: C 542 MET cc_start: 0.6229 (mmp) cc_final: 0.5732 (mmp) REVERT: C 572 LYS cc_start: 0.9002 (tptp) cc_final: 0.8705 (tptp) REVERT: D 20 HIS cc_start: 0.6634 (OUTLIER) cc_final: 0.6174 (t-90) outliers start: 42 outliers final: 23 residues processed: 116 average time/residue: 0.2633 time to fit residues: 44.5639 Evaluate side-chains 108 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 20 HIS Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 15 optimal weight: 30.0000 chunk 65 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 138 optimal weight: 0.0980 chunk 146 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN A 523 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12813 Z= 0.291 Angle : 0.620 9.731 17239 Z= 0.328 Chirality : 0.042 0.313 1894 Planarity : 0.004 0.079 2194 Dihedral : 8.611 88.852 1741 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.03 % Allowed : 13.11 % Favored : 82.85 % 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: 0.37 (0.22), residues: 1524 helix: 1.19 (0.21), residues: 629 sheet: 0.23 (0.38), residues: 208 loop : -0.59 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 423 HIS 0.014 0.002 HIS D 20 PHE 0.013 0.002 PHE B 133 TYR 0.019 0.002 TYR A 372 ARG 0.007 0.001 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 83 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8345 (OUTLIER) cc_final: 0.7950 (p) REVERT: A 123 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7115 (mm) REVERT: A 125 MET cc_start: 0.8233 (mmm) cc_final: 0.7124 (mmp) REVERT: B 622 LYS cc_start: 0.7462 (tptt) cc_final: 0.6967 (tptt) REVERT: C 572 LYS cc_start: 0.9059 (tptp) cc_final: 0.8609 (tttt) REVERT: D 14 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7102 (p0) outliers start: 56 outliers final: 37 residues processed: 130 average time/residue: 0.2547 time to fit residues: 48.1856 Evaluate side-chains 121 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 81 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 20 HIS Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 125 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12813 Z= 0.218 Angle : 0.596 9.198 17239 Z= 0.310 Chirality : 0.042 0.371 1894 Planarity : 0.004 0.079 2194 Dihedral : 8.466 89.492 1741 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.60 % Allowed : 14.05 % Favored : 82.35 % 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: 0.38 (0.22), residues: 1524 helix: 1.23 (0.21), residues: 632 sheet: 0.13 (0.38), residues: 207 loop : -0.58 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 7 HIS 0.006 0.001 HIS A 314 PHE 0.011 0.001 PHE B 133 TYR 0.017 0.001 TYR A 372 ARG 0.008 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 86 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.7958 (p) REVERT: A 123 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7441 (mm) REVERT: B 125 MET cc_start: 0.8555 (mmm) cc_final: 0.7209 (mmm) REVERT: B 193 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8014 (mm) REVERT: B 524 MET cc_start: 0.9332 (tpt) cc_final: 0.9110 (tpt) REVERT: B 622 LYS cc_start: 0.7564 (tptt) cc_final: 0.7063 (tptt) REVERT: C 572 LYS cc_start: 0.9038 (tptp) cc_final: 0.8600 (tttt) REVERT: D 14 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.7027 (p0) outliers start: 50 outliers final: 34 residues processed: 123 average time/residue: 0.2632 time to fit residues: 47.1453 Evaluate side-chains 120 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 82 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 560 MET Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12813 Z= 0.226 Angle : 0.609 11.337 17239 Z= 0.314 Chirality : 0.041 0.311 1894 Planarity : 0.004 0.080 2194 Dihedral : 8.445 89.805 1741 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.75 % Allowed : 15.27 % Favored : 80.98 % 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: 0.32 (0.22), residues: 1524 helix: 1.20 (0.21), residues: 632 sheet: 0.09 (0.38), residues: 205 loop : -0.63 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 7 HIS 0.006 0.001 HIS A 314 PHE 0.015 0.002 PHE D 124 TYR 0.017 0.001 TYR A 372 ARG 0.008 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 84 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8007 (p) REVERT: A 123 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7476 (mm) REVERT: A 601 MET cc_start: 0.6297 (tpp) cc_final: 0.5961 (tpp) REVERT: B 193 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8070 (mm) REVERT: B 332 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7984 (mt) REVERT: B 524 MET cc_start: 0.9337 (tpt) cc_final: 0.9096 (tpt) REVERT: B 622 LYS cc_start: 0.7577 (tptt) cc_final: 0.6980 (tptt) REVERT: C 542 MET cc_start: 0.6226 (mmp) cc_final: 0.5692 (mmp) REVERT: C 572 LYS cc_start: 0.9050 (tptp) cc_final: 0.8742 (tptp) REVERT: D 14 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6843 (p0) outliers start: 52 outliers final: 36 residues processed: 126 average time/residue: 0.2655 time to fit residues: 48.6419 Evaluate side-chains 123 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 82 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 83 optimal weight: 0.4980 chunk 107 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12813 Z= 0.174 Angle : 0.590 10.762 17239 Z= 0.301 Chirality : 0.041 0.364 1894 Planarity : 0.004 0.079 2194 Dihedral : 8.260 88.214 1741 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.24 % Allowed : 15.42 % Favored : 81.34 % 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: 0.39 (0.22), residues: 1524 helix: 1.27 (0.21), residues: 635 sheet: 0.03 (0.37), residues: 207 loop : -0.58 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 7 HIS 0.005 0.001 HIS B 146 PHE 0.010 0.001 PHE C 525 TYR 0.018 0.001 TYR B 428 ARG 0.009 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 86 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.7986 (p) REVERT: A 123 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7353 (mm) REVERT: B 193 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8089 (mm) REVERT: B 524 MET cc_start: 0.9318 (tpt) cc_final: 0.9052 (tpt) REVERT: C 457 ASP cc_start: 0.8868 (t70) cc_final: 0.8448 (t70) REVERT: C 572 LYS cc_start: 0.9047 (tptp) cc_final: 0.8572 (tttt) REVERT: D 20 HIS cc_start: 0.6489 (OUTLIER) cc_final: 0.6179 (t-170) REVERT: D 105 MET cc_start: 0.3572 (tpp) cc_final: 0.1816 (mtp) outliers start: 45 outliers final: 33 residues processed: 119 average time/residue: 0.2472 time to fit residues: 42.7995 Evaluate side-chains 120 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 83 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 560 MET Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 20 HIS Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12813 Z= 0.185 Angle : 0.605 10.936 17239 Z= 0.306 Chirality : 0.042 0.369 1894 Planarity : 0.004 0.080 2194 Dihedral : 8.196 87.758 1741 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.95 % Allowed : 16.07 % Favored : 80.98 % 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: 0.38 (0.22), residues: 1524 helix: 1.26 (0.21), residues: 635 sheet: 0.07 (0.37), residues: 206 loop : -0.59 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 7 HIS 0.005 0.001 HIS A 314 PHE 0.019 0.001 PHE B 113 TYR 0.015 0.001 TYR B 428 ARG 0.009 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 85 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8001 (p) REVERT: A 123 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7324 (mm) REVERT: B 125 MET cc_start: 0.8811 (mmm) cc_final: 0.7932 (mmm) REVERT: B 193 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8185 (mm) REVERT: B 524 MET cc_start: 0.9317 (tpt) cc_final: 0.9038 (tpt) REVERT: C 572 LYS cc_start: 0.9040 (tptp) cc_final: 0.8557 (tttt) REVERT: D 20 HIS cc_start: 0.6601 (OUTLIER) cc_final: 0.6245 (t-170) REVERT: D 39 ARG cc_start: 0.8820 (ttp80) cc_final: 0.8299 (tmm-80) outliers start: 41 outliers final: 32 residues processed: 117 average time/residue: 0.2675 time to fit residues: 45.6109 Evaluate side-chains 117 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 81 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 20 HIS Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 144 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 GLN D 9 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12813 Z= 0.273 Angle : 0.677 12.032 17239 Z= 0.345 Chirality : 0.043 0.378 1894 Planarity : 0.004 0.082 2194 Dihedral : 8.363 87.166 1741 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.24 % Allowed : 15.85 % Favored : 80.91 % 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: 0.13 (0.22), residues: 1524 helix: 1.00 (0.21), residues: 644 sheet: -0.02 (0.38), residues: 196 loop : -0.71 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 7 HIS 0.008 0.002 HIS C 477 PHE 0.017 0.002 PHE B 113 TYR 0.019 0.002 TYR A 372 ARG 0.007 0.001 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 86 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8057 (p) REVERT: B 114 MET cc_start: 0.8837 (mtt) cc_final: 0.8592 (mmm) REVERT: B 125 MET cc_start: 0.8790 (mmm) cc_final: 0.7764 (mmm) REVERT: B 193 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8128 (mm) REVERT: B 524 MET cc_start: 0.9343 (tpt) cc_final: 0.8798 (tpp) REVERT: C 572 LYS cc_start: 0.9072 (tptp) cc_final: 0.8583 (tttt) REVERT: D 20 HIS cc_start: 0.6705 (OUTLIER) cc_final: 0.6364 (t-170) REVERT: D 39 ARG cc_start: 0.8836 (ttp80) cc_final: 0.8368 (tmm-80) outliers start: 45 outliers final: 36 residues processed: 122 average time/residue: 0.2839 time to fit residues: 49.8906 Evaluate side-chains 125 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 86 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 20 HIS Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 139 optimal weight: 30.0000 chunk 120 optimal weight: 30.0000 chunk 12 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12813 Z= 0.280 Angle : 0.699 12.499 17239 Z= 0.355 Chirality : 0.043 0.382 1894 Planarity : 0.004 0.084 2194 Dihedral : 8.409 88.199 1741 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 25.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.95 % Allowed : 16.57 % Favored : 80.48 % 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: 0.03 (0.22), residues: 1524 helix: 0.93 (0.21), residues: 642 sheet: -0.09 (0.38), residues: 195 loop : -0.76 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 7 HIS 0.007 0.002 HIS A 314 PHE 0.023 0.002 PHE D 43 TYR 0.020 0.002 TYR A 372 ARG 0.007 0.001 ARG D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 87 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8020 (p) REVERT: B 125 MET cc_start: 0.8776 (mmm) cc_final: 0.7943 (mmm) REVERT: B 193 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8171 (mm) REVERT: B 524 MET cc_start: 0.9353 (tpt) cc_final: 0.8834 (tpp) REVERT: C 572 LYS cc_start: 0.9047 (tptp) cc_final: 0.8544 (tttt) REVERT: D 20 HIS cc_start: 0.6743 (OUTLIER) cc_final: 0.6407 (t-170) REVERT: D 39 ARG cc_start: 0.8851 (ttp80) cc_final: 0.8337 (tmm-80) outliers start: 41 outliers final: 34 residues processed: 120 average time/residue: 0.2635 time to fit residues: 45.5013 Evaluate side-chains 122 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 85 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 20 HIS Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 5.9990 chunk 111 optimal weight: 0.0980 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 124 optimal weight: 0.0030 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 ASN ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 HIS D 20 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.053629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.040201 restraints weight = 120886.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.040901 restraints weight = 92185.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.041203 restraints weight = 77622.003| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12813 Z= 0.162 Angle : 0.648 12.156 17239 Z= 0.325 Chirality : 0.042 0.353 1894 Planarity : 0.004 0.082 2194 Dihedral : 8.147 87.331 1741 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.23 % Allowed : 17.22 % Favored : 80.55 % 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: 0.35 (0.22), residues: 1524 helix: 1.18 (0.21), residues: 639 sheet: 0.10 (0.38), residues: 203 loop : -0.57 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 7 HIS 0.004 0.001 HIS B 314 PHE 0.018 0.001 PHE B 113 TYR 0.015 0.001 TYR B 428 ARG 0.010 0.000 ARG D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2284.76 seconds wall clock time: 42 minutes 15.89 seconds (2535.89 seconds total)