Starting phenix.real_space_refine on Sat Jul 27 01:46:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3l_18872/07_2024/8r3l_18872.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3l_18872/07_2024/8r3l_18872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3l_18872/07_2024/8r3l_18872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3l_18872/07_2024/8r3l_18872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3l_18872/07_2024/8r3l_18872.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r3l_18872/07_2024/8r3l_18872.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 33 5.49 5 S 126 5.16 5 C 11144 2.51 5 N 3117 2.21 5 O 3458 1.98 5 H 17553 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A GLU 597": "OE1" <-> "OE2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B GLU 387": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "B GLU 656": "OE1" <-> "OE2" Residue "B GLU 731": "OE1" <-> "OE2" Residue "B GLU 751": "OE1" <-> "OE2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 35431 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 708, 11437 Classifications: {'peptide': 708} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 675} Chain breaks: 1 Chain: "B" Number of atoms: 11774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 11774 Classifications: {'peptide': 740} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 707} Chain breaks: 1 Chain: "C" Number of atoms: 10917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 10917 Classifications: {'peptide': 677} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 649} Chain: "R" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 438 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 1, 'rna3p_pyr': 9} Link IDs: {'rna2p': 4, 'rna3p': 10} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "V" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 527 Classifications: {'RNA': 16} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 12} Chain: "G" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 338 Classifications: {'peptide': 24} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 16} Time building chain proxies: 16.83, per 1000 atoms: 0.48 Number of scatterers: 35431 At special positions: 0 Unit cell: (105, 128.52, 144.48, 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 126 16.00 P 33 15.00 O 3458 8.00 N 3117 7.00 C 11144 6.00 H 17553 1.00 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: 29.39 Conformation dependent library (CDL) restraints added in 3.1 seconds 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4058 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 23 sheets defined 49.2% alpha, 14.1% beta 5 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 16.04 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.689A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.718A pdb=" N PHE A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 350 removed outlier: 3.562A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.956A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 529 through 538 Proline residue: A 534 - end of helix removed outlier: 3.684A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 602 removed outlier: 4.118A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 633 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 4.123A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.526A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 715 removed outlier: 3.514A pdb=" N LEU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.653A pdb=" N ILE B 18 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.506A pdb=" N GLN B 115 " --> pdb=" O MET B 111 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.548A pdb=" N GLN B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 162 through 176 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.657A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 291 removed outlier: 3.516A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.545A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 371 through 376 removed outlier: 4.102A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 474 Processing helix chain 'B' and resid 505 through 512 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 672 through 678 removed outlier: 6.588A pdb=" N SER B 678 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 700 removed outlier: 4.155A pdb=" N LEU B 683 " --> pdb=" O GLN B 679 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 733 Processing helix chain 'B' and resid 736 through 756 removed outlier: 3.666A pdb=" N ARG B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN B 756 " --> pdb=" O GLU B 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 removed outlier: 3.848A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 92 through 103 removed outlier: 4.140A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 removed outlier: 4.397A pdb=" N LYS C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 172 Processing helix chain 'C' and resid 179 through 194 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 251 through 272 removed outlier: 4.061A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 305 through 316 Processing helix chain 'C' and resid 390 through 405 Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 429 through 441 Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 514 through 518 Processing helix chain 'C' and resid 541 through 556 Processing helix chain 'C' and resid 556 through 567 Processing helix chain 'C' and resid 567 through 573 removed outlier: 3.677A pdb=" N LEU C 571 " --> pdb=" O ASP C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 582 Processing helix chain 'C' and resid 585 through 606 removed outlier: 4.348A pdb=" N GLY C 590 " --> pdb=" O LYS C 586 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C 595 " --> pdb=" O GLN C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 620 through 624 removed outlier: 3.909A pdb=" N ALA C 623 " --> pdb=" O PRO C 620 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA C 624 " --> pdb=" O PHE C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 620 through 624' Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 removed outlier: 4.010A pdb=" N LYS A 73 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 3.666A pdb=" N THR A 123 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 6.279A pdb=" N ARG A 496 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR A 491 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 324 removed outlier: 11.609A pdb=" N LYS A 318 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N MET A 548 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N GLY A 546 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU A 544 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG A 496 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR A 491 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N THR A 498 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N CYS A 489 " --> pdb=" O THR A 498 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 379 removed outlier: 5.710A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL A 379 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 628 through 632 removed outlier: 6.741A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 185 Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.783A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 492 removed outlier: 4.539A pdb=" N PHE B 496 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 642 through 645 Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.571A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 135 removed outlier: 5.918A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB8, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AB9, first strand: chain 'C' and resid 323 through 325 removed outlier: 6.930A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR C 371 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL C 386 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE C 373 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU C 384 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG C 375 " --> pdb=" O ILE C 382 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 339 through 345 Processing sheet with id=AC2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AC3, first strand: chain 'C' and resid 497 through 498 removed outlier: 6.810A pdb=" N VAL C 504 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 635 through 640 Processing sheet with id=AC5, first strand: chain 'C' and resid 657 through 659 removed outlier: 6.008A pdb=" N LEU C 665 " --> pdb=" O ALA C 672 " (cutoff:3.500A) 869 hydrogen bonds defined for protein. 2400 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 14 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 14.72 Time building geometry restraints manager: 30.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17521 1.03 - 1.23: 227 1.23 - 1.43: 7436 1.43 - 1.62: 10442 1.62 - 1.82: 220 Bond restraints: 35846 Sorted by residual: bond pdb=" N TYR G 3 " pdb=" H1 TYR G 3 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N MET A 1 " pdb=" H MET A 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" CA ILE C 147 " pdb=" CB ILE C 147 " ideal model delta sigma weight residual 1.528 1.543 -0.015 1.34e-02 5.57e+03 1.24e+00 bond pdb=" C SER B 444 " pdb=" O SER B 444 " ideal model delta sigma weight residual 1.243 1.235 0.009 9.50e-03 1.11e+04 8.18e-01 ... (remaining 35841 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.49: 671 106.49 - 113.37: 42126 113.37 - 120.25: 11762 120.25 - 127.13: 9974 127.13 - 134.01: 246 Bond angle restraints: 64779 Sorted by residual: angle pdb=" C SER B 444 " pdb=" CA SER B 444 " pdb=" CB SER B 444 " ideal model delta sigma weight residual 117.23 111.21 6.02 1.36e+00 5.41e-01 1.96e+01 angle pdb=" CB MET A 86 " pdb=" CG MET A 86 " pdb=" SD MET A 86 " ideal model delta sigma weight residual 112.70 121.87 -9.17 3.00e+00 1.11e-01 9.34e+00 angle pdb=" CA SER B 444 " pdb=" C SER B 444 " pdb=" N ASP B 445 " ideal model delta sigma weight residual 119.98 117.57 2.41 8.50e-01 1.38e+00 8.02e+00 angle pdb=" CG MET A 86 " pdb=" SD MET A 86 " pdb=" CE MET A 86 " ideal model delta sigma weight residual 100.90 105.89 -4.99 2.20e+00 2.07e-01 5.15e+00 angle pdb=" CB MET C 206 " pdb=" CG MET C 206 " pdb=" SD MET C 206 " ideal model delta sigma weight residual 112.70 118.94 -6.24 3.00e+00 1.11e-01 4.33e+00 ... (remaining 64774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14787 17.94 - 35.88: 1422 35.88 - 53.82: 487 53.82 - 71.76: 129 71.76 - 89.70: 35 Dihedral angle restraints: 16860 sinusoidal: 9597 harmonic: 7263 Sorted by residual: dihedral pdb=" CA PHE A 612 " pdb=" C PHE A 612 " pdb=" N GLU A 613 " pdb=" CA GLU A 613 " ideal model delta harmonic sigma weight residual 180.00 152.52 27.48 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ASP A 386 " pdb=" CB ASP A 386 " pdb=" CG ASP A 386 " pdb=" OD1 ASP A 386 " ideal model delta sinusoidal sigma weight residual -30.00 -89.55 59.55 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CB GLU A 252 " pdb=" CG GLU A 252 " pdb=" CD GLU A 252 " pdb=" OE1 GLU A 252 " ideal model delta sinusoidal sigma weight residual 0.00 -89.70 89.70 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 16857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2393 0.052 - 0.104: 291 0.104 - 0.155: 71 0.155 - 0.207: 0 0.207 - 0.259: 1 Chirality restraints: 2756 Sorted by residual: chirality pdb=" P U R 18 " pdb=" OP1 U R 18 " pdb=" OP2 U R 18 " pdb=" O5' U R 18 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE A 354 " pdb=" N ILE A 354 " pdb=" C ILE A 354 " pdb=" CB ILE A 354 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE C 647 " pdb=" N ILE C 647 " pdb=" C ILE C 647 " pdb=" CB ILE C 647 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 2753 not shown) Planarity restraints: 5157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 571 " 0.214 9.50e-02 1.11e+02 7.16e-02 6.37e+00 pdb=" NE ARG B 571 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 571 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 571 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 571 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B 571 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B 571 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 571 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG B 571 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 148 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO C 149 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.022 2.00e-02 2.50e+03 9.09e-03 2.68e+00 pdb=" N9 A V 4 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A V 4 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" H8 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" H2 A V 4 " 0.001 2.00e-02 2.50e+03 ... (remaining 5154 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 1110 2.14 - 2.75: 65361 2.75 - 3.37: 102646 3.37 - 3.98: 132126 3.98 - 4.60: 207843 Nonbonded interactions: 509086 Sorted by model distance: nonbonded pdb=" OE1 GLU A 610 " pdb=" H GLU A 610 " model vdw 1.519 1.850 nonbonded pdb=" OE1 GLU A 243 " pdb=" H GLU A 243 " model vdw 1.521 1.850 nonbonded pdb=" OE1 GLU A 206 " pdb=" H GLU A 206 " model vdw 1.582 1.850 nonbonded pdb=" OD1 ASN C 148 " pdb=" H LYS C 214 " model vdw 1.587 1.850 nonbonded pdb=" O MET B 409 " pdb=" H22 G R 16 " model vdw 1.592 1.850 ... (remaining 509081 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.550 Extract box with map and model: 1.560 Check model and map are aligned: 0.290 Set scattering table: 0.360 Process input model: 126.820 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.002 0.034 18293 Z= 0.164 Angle : 0.475 9.170 24830 Z= 0.250 Chirality : 0.038 0.259 2756 Planarity : 0.003 0.095 3092 Dihedral : 17.480 89.696 7198 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.21 % Allowed : 17.91 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.70 (0.19), residues: 2131 helix: 1.60 (0.17), residues: 956 sheet: 0.23 (0.31), residues: 271 loop : -0.66 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 557 HIS 0.003 0.001 HIS A 41 PHE 0.021 0.001 PHE A 612 TYR 0.011 0.001 TYR G 17 ARG 0.015 0.000 ARG B 571 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 194 time to evaluate : 2.898 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: C 483 MET cc_start: 0.4067 (mmt) cc_final: 0.3699 (mmm) REVERT: C 493 ARG cc_start: 0.5071 (mmt-90) cc_final: 0.4690 (mtm-85) outliers start: 4 outliers final: 3 residues processed: 198 average time/residue: 0.7554 time to fit residues: 222.1693 Evaluate side-chains 190 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain C residue 537 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18293 Z= 0.272 Angle : 0.511 5.135 24830 Z= 0.271 Chirality : 0.039 0.161 2756 Planarity : 0.004 0.039 3092 Dihedral : 10.225 74.748 2829 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.62 % Allowed : 16.75 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.55 (0.18), residues: 2131 helix: 1.56 (0.17), residues: 972 sheet: 0.22 (0.32), residues: 253 loop : -0.91 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 78 HIS 0.006 0.001 HIS C 27 PHE 0.027 0.001 PHE A 612 TYR 0.014 0.001 TYR G 17 ARG 0.004 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 194 time to evaluate : 2.816 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 292 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8335 (pp) REVERT: B 707 ARG cc_start: 0.7485 (mtm110) cc_final: 0.7182 (mtt180) REVERT: C 493 ARG cc_start: 0.5043 (mmt-90) cc_final: 0.4639 (mtm-85) REVERT: C 522 GLN cc_start: 0.6116 (mt0) cc_final: 0.5453 (mp10) outliers start: 31 outliers final: 20 residues processed: 218 average time/residue: 0.7348 time to fit residues: 239.4403 Evaluate side-chains 207 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain G residue 4 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 195 optimal weight: 0.0270 chunk 211 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 641 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18293 Z= 0.172 Angle : 0.461 5.503 24830 Z= 0.241 Chirality : 0.038 0.150 2756 Planarity : 0.003 0.041 3092 Dihedral : 10.153 74.157 2827 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.36 % Allowed : 17.64 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2131 helix: 1.71 (0.17), residues: 972 sheet: 0.18 (0.31), residues: 259 loop : -0.93 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 537 HIS 0.003 0.001 HIS C 27 PHE 0.025 0.001 PHE A 612 TYR 0.013 0.001 TYR G 17 ARG 0.003 0.000 ARG B 571 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 2.645 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: B 707 ARG cc_start: 0.7498 (mtm110) cc_final: 0.7180 (mtt180) REVERT: C 64 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8323 (mtp) REVERT: C 493 ARG cc_start: 0.4999 (mmt-90) cc_final: 0.4559 (mtm-85) REVERT: C 522 GLN cc_start: 0.6265 (mt0) cc_final: 0.5545 (mp10) outliers start: 26 outliers final: 22 residues processed: 208 average time/residue: 0.7205 time to fit residues: 223.1795 Evaluate side-chains 211 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN B 306 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18293 Z= 0.216 Angle : 0.474 4.842 24830 Z= 0.249 Chirality : 0.038 0.161 2756 Planarity : 0.003 0.038 3092 Dihedral : 10.140 73.726 2827 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.94 % Allowed : 17.33 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.56 (0.18), residues: 2131 helix: 1.67 (0.17), residues: 973 sheet: 0.12 (0.31), residues: 259 loop : -1.01 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 577 HIS 0.003 0.001 HIS C 27 PHE 0.027 0.001 PHE A 612 TYR 0.014 0.001 TYR G 17 ARG 0.003 0.000 ARG B 571 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 2.823 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 292 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8329 (pp) REVERT: B 707 ARG cc_start: 0.7511 (mtm110) cc_final: 0.7171 (mtt180) REVERT: C 64 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8332 (mtp) REVERT: C 522 GLN cc_start: 0.6331 (mt0) cc_final: 0.5611 (mp10) REVERT: C 595 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7354 (t80) outliers start: 37 outliers final: 27 residues processed: 211 average time/residue: 0.7253 time to fit residues: 228.0253 Evaluate side-chains 213 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 2.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 595 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18293 Z= 0.274 Angle : 0.502 4.918 24830 Z= 0.266 Chirality : 0.039 0.181 2756 Planarity : 0.004 0.041 3092 Dihedral : 10.206 73.687 2827 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.36 % Allowed : 17.80 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.34 (0.18), residues: 2131 helix: 1.52 (0.17), residues: 973 sheet: -0.05 (0.32), residues: 251 loop : -1.13 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 577 HIS 0.005 0.001 HIS C 27 PHE 0.033 0.001 PHE A 612 TYR 0.016 0.001 TYR G 17 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 189 time to evaluate : 3.182 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 83 ASP cc_start: 0.7102 (t0) cc_final: 0.6624 (t0) REVERT: A 125 ARG cc_start: 0.2493 (OUTLIER) cc_final: 0.1936 (mtt-85) REVERT: A 292 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8305 (pp) REVERT: A 677 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: C 64 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8294 (mtp) REVERT: C 493 ARG cc_start: 0.5128 (mmt-90) cc_final: 0.4657 (mtm-85) REVERT: C 522 GLN cc_start: 0.6478 (mt0) cc_final: 0.5671 (mp10) REVERT: C 595 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7325 (t80) outliers start: 45 outliers final: 35 residues processed: 222 average time/residue: 0.7506 time to fit residues: 247.9519 Evaluate side-chains 225 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 185 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 702 SER Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 595 PHE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 306 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 18293 Z= 0.303 Angle : 0.510 5.693 24830 Z= 0.271 Chirality : 0.040 0.187 2756 Planarity : 0.004 0.039 3092 Dihedral : 10.241 73.617 2827 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.36 % Allowed : 17.80 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.19 (0.18), residues: 2131 helix: 1.41 (0.16), residues: 975 sheet: -0.15 (0.32), residues: 251 loop : -1.23 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 577 HIS 0.004 0.001 HIS C 27 PHE 0.035 0.001 PHE A 612 TYR 0.017 0.001 TYR G 17 ARG 0.004 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 190 time to evaluate : 3.044 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 83 ASP cc_start: 0.7136 (t0) cc_final: 0.6657 (t0) REVERT: A 125 ARG cc_start: 0.2582 (OUTLIER) cc_final: 0.2026 (mtt-85) REVERT: A 292 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8327 (pp) REVERT: A 677 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: C 64 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8259 (mtp) REVERT: C 522 GLN cc_start: 0.6622 (mt0) cc_final: 0.5743 (mp10) REVERT: C 595 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.7344 (t80) outliers start: 45 outliers final: 35 residues processed: 224 average time/residue: 0.7786 time to fit residues: 254.2542 Evaluate side-chains 226 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 186 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 595 PHE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 306 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18293 Z= 0.208 Angle : 0.477 5.186 24830 Z= 0.251 Chirality : 0.038 0.174 2756 Planarity : 0.004 0.041 3092 Dihedral : 10.196 73.615 2827 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.46 % Allowed : 18.01 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.33 (0.18), residues: 2131 helix: 1.53 (0.17), residues: 975 sheet: -0.07 (0.31), residues: 256 loop : -1.18 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 577 HIS 0.003 0.001 HIS C 27 PHE 0.032 0.001 PHE A 612 TYR 0.015 0.001 TYR G 17 ARG 0.003 0.000 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 186 time to evaluate : 2.870 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 83 ASP cc_start: 0.7146 (t0) cc_final: 0.6673 (t0) REVERT: A 125 ARG cc_start: 0.2572 (OUTLIER) cc_final: 0.2148 (mtp180) REVERT: A 292 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8321 (pp) REVERT: A 677 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: B 707 ARG cc_start: 0.7459 (mtm110) cc_final: 0.7165 (mtt180) REVERT: C 64 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8258 (mtp) REVERT: C 493 ARG cc_start: 0.5154 (mmt-90) cc_final: 0.4669 (mtm-85) REVERT: C 522 GLN cc_start: 0.6677 (mt0) cc_final: 0.5762 (mp10) REVERT: C 595 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.7315 (t80) outliers start: 47 outliers final: 37 residues processed: 222 average time/residue: 0.7452 time to fit residues: 245.0728 Evaluate side-chains 229 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 187 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 213 ARG Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 595 PHE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18293 Z= 0.232 Angle : 0.485 5.742 24830 Z= 0.256 Chirality : 0.039 0.178 2756 Planarity : 0.004 0.049 3092 Dihedral : 10.202 73.522 2827 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.46 % Allowed : 18.12 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.30 (0.18), residues: 2131 helix: 1.51 (0.17), residues: 976 sheet: 0.01 (0.31), residues: 251 loop : -1.23 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 577 HIS 0.004 0.001 HIS C 27 PHE 0.033 0.001 PHE A 612 TYR 0.015 0.001 TYR G 17 ARG 0.003 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 190 time to evaluate : 2.740 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 125 ARG cc_start: 0.2520 (OUTLIER) cc_final: 0.2124 (mtp180) REVERT: A 292 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8322 (pp) REVERT: A 677 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: B 707 ARG cc_start: 0.7441 (mtm110) cc_final: 0.7125 (mtt180) REVERT: C 493 ARG cc_start: 0.5139 (mmt-90) cc_final: 0.4626 (mtm-85) REVERT: C 522 GLN cc_start: 0.6745 (mt0) cc_final: 0.6103 (tp40) REVERT: C 595 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.7281 (t80) outliers start: 47 outliers final: 39 residues processed: 227 average time/residue: 0.7811 time to fit residues: 260.1720 Evaluate side-chains 228 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 185 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 595 PHE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 151 optimal weight: 0.0030 chunk 59 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18293 Z= 0.302 Angle : 0.521 5.943 24830 Z= 0.277 Chirality : 0.040 0.194 2756 Planarity : 0.004 0.044 3092 Dihedral : 10.208 73.449 2823 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.62 % Allowed : 18.17 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.11 (0.18), residues: 2131 helix: 1.37 (0.16), residues: 978 sheet: -0.10 (0.31), residues: 251 loop : -1.34 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 309 HIS 0.004 0.001 HIS C 27 PHE 0.037 0.001 PHE A 612 TYR 0.018 0.001 TYR G 17 ARG 0.005 0.000 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 188 time to evaluate : 2.790 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 125 ARG cc_start: 0.2493 (OUTLIER) cc_final: 0.2096 (mtp180) REVERT: A 292 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8317 (pp) REVERT: A 677 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: B 707 ARG cc_start: 0.7434 (mtm110) cc_final: 0.7109 (mtt180) REVERT: C 318 ARG cc_start: 0.7443 (mtt180) cc_final: 0.6568 (ptt180) REVERT: C 522 GLN cc_start: 0.6834 (mt0) cc_final: 0.6109 (tp40) REVERT: C 595 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7319 (t80) outliers start: 50 outliers final: 42 residues processed: 228 average time/residue: 0.7411 time to fit residues: 252.2288 Evaluate side-chains 233 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 187 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 595 PHE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 214 optimal weight: 0.1980 chunk 197 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS B 306 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18293 Z= 0.180 Angle : 0.478 6.365 24830 Z= 0.251 Chirality : 0.038 0.171 2756 Planarity : 0.003 0.047 3092 Dihedral : 10.118 73.502 2823 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.25 % Allowed : 18.48 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.34 (0.18), residues: 2131 helix: 1.58 (0.17), residues: 976 sheet: 0.00 (0.31), residues: 251 loop : -1.24 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 557 HIS 0.004 0.001 HIS A 74 PHE 0.032 0.001 PHE A 612 TYR 0.014 0.001 TYR G 17 ARG 0.003 0.000 ARG A 496 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4262 Ramachandran restraints generated. 2131 Oldfield, 0 Emsley, 2131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 189 time to evaluate : 3.037 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 125 ARG cc_start: 0.2427 (OUTLIER) cc_final: 0.2076 (mtp180) REVERT: A 292 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8300 (pp) REVERT: A 677 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: B 148 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7392 (mp0) REVERT: B 707 ARG cc_start: 0.7412 (mtm110) cc_final: 0.7111 (mtt180) REVERT: C 318 ARG cc_start: 0.7430 (mtt180) cc_final: 0.6559 (ptt180) REVERT: C 522 GLN cc_start: 0.6823 (mt0) cc_final: 0.6084 (tp40) REVERT: C 595 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.7288 (t80) outliers start: 43 outliers final: 38 residues processed: 222 average time/residue: 0.7296 time to fit residues: 240.6601 Evaluate side-chains 225 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 646 MET Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 718 MET Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 466 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 537 TRP Chi-restraints excluded: chain C residue 595 PHE Chi-restraints excluded: chain G residue 4 SER Chi-restraints excluded: chain G residue 11 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 157 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 71 optimal weight: 0.0870 chunk 175 optimal weight: 6.9990 chunk 21 optimal weight: 0.0770 chunk 31 optimal weight: 0.8980 chunk 149 optimal weight: 0.1980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS B 306 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.139602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.102230 restraints weight = 89168.678| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.14 r_work: 0.3219 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18293 Z= 0.129 Angle : 0.463 7.755 24830 Z= 0.240 Chirality : 0.037 0.147 2756 Planarity : 0.003 0.039 3092 Dihedral : 9.974 73.510 2823 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.26 % Allowed : 19.84 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % 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: 0.63 (0.18), residues: 2131 helix: 1.81 (0.17), residues: 978 sheet: 0.04 (0.32), residues: 256 loop : -1.06 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 557 HIS 0.004 0.001 HIS A 74 PHE 0.026 0.001 PHE A 612 TYR 0.011 0.001 TYR G 17 ARG 0.003 0.000 ARG A 496 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7730.12 seconds wall clock time: 135 minutes 27.27 seconds (8127.27 seconds total)