Starting phenix.real_space_refine on Sat Feb 17 12:32:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tw1_10603/02_2024/6tw1_10603_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tw1_10603/02_2024/6tw1_10603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tw1_10603/02_2024/6tw1_10603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tw1_10603/02_2024/6tw1_10603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tw1_10603/02_2024/6tw1_10603_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tw1_10603/02_2024/6tw1_10603_updated.pdb" } resolution = 2.7 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= 0.000 sd= 0.005 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 45 5.49 5 Mg 4 5.21 5 S 108 5.16 5 C 11508 2.51 5 N 3231 2.21 5 O 3731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 64": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A ARG 503": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 571": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 707": "NH1" <-> "NH2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C ARG 427": "NH1" <-> "NH2" Residue "C ARG 737": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18627 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5733 Classifications: {'peptide': 703} Link IDs: {'PTRANS': 25, 'TRANS': 677} Chain breaks: 2 Chain: "B" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5925 Classifications: {'peptide': 740} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 711} Chain breaks: 1 Chain: "C" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5879 Classifications: {'peptide': 740} Link IDs: {'PTRANS': 30, 'TRANS': 709} Chain: "V" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 703 Classifications: {'RNA': 33} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 14, 'rna3p': 18} Chain breaks: 1 Chain: "M" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 4} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Unusual residues: {' MG': 2, 'M4H': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 11 Unusual residues: {' MG': 2, 'POP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "V" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 10.62, per 1000 atoms: 0.57 Number of scatterers: 18627 At special positions: 0 Unit cell: (121.092, 122.718, 119.467, 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 108 16.00 P 45 15.00 Mg 4 11.99 O 3731 8.00 N 3231 7.00 C 11508 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: 7.71 Conformation dependent library (CDL) restraints added in 3.8 seconds 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 23 sheets defined 40.9% alpha, 11.5% beta 12 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 10.03 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 11 through 23 Processing helix chain 'A' and resid 32 through 47 Processing helix chain 'A' and resid 84 through 97 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 165 through 184 Processing helix chain 'A' and resid 189 through 192 No H-bonds generated for 'chain 'A' and resid 189 through 192' Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.979A pdb=" N THR A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 346 Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.506A pdb=" N SER A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 445 removed outlier: 3.722A pdb=" N PHE A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 470 Processing helix chain 'A' and resid 529 through 532 Processing helix chain 'A' and resid 567 through 573 Processing helix chain 'A' and resid 576 through 598 removed outlier: 4.103A pdb=" N SER A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN A 585 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU A 588 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A 594 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS A 598 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 628 through 644 Processing helix chain 'A' and resid 648 through 668 removed outlier: 4.211A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 688 removed outlier: 4.297A pdb=" N CYS A 688 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 712 Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 15 through 21 removed outlier: 5.904A pdb=" N SER B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 102 through 114 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.915A pdb=" N PHE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 246 through 265 removed outlier: 4.369A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 315 through 325 Processing helix chain 'B' and resid 331 through 337 Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 378 through 380 No H-bonds generated for 'chain 'B' and resid 378 through 380' Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.098A pdb=" N GLY B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 506 through 511 Proline residue: B 510 - end of helix Processing helix chain 'B' and resid 519 through 536 Processing helix chain 'B' and resid 541 through 558 Processing helix chain 'B' and resid 573 through 581 Processing helix chain 'B' and resid 586 through 588 No H-bonds generated for 'chain 'B' and resid 586 through 588' Processing helix chain 'B' and resid 591 through 593 No H-bonds generated for 'chain 'B' and resid 591 through 593' Processing helix chain 'B' and resid 608 through 611 No H-bonds generated for 'chain 'B' and resid 608 through 611' Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 680 through 697 removed outlier: 5.205A pdb=" N ASP B 685 " --> pdb=" O GLY B 681 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU B 686 " --> pdb=" O ILE B 682 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 687 " --> pdb=" O LEU B 683 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 697 " --> pdb=" O CYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 703 No H-bonds generated for 'chain 'B' and resid 701 through 703' Processing helix chain 'B' and resid 714 through 731 Processing helix chain 'B' and resid 737 through 755 Processing helix chain 'C' and resid 1 through 11 Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 25 through 31 removed outlier: 3.870A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 removed outlier: 4.366A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 93 through 102 Processing helix chain 'C' and resid 111 through 114 No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 116 through 126 Processing helix chain 'C' and resid 156 through 167 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 180 through 192 Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 226 through 229 No H-bonds generated for 'chain 'C' and resid 226 through 229' Processing helix chain 'C' and resid 232 through 235 No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 252 through 272 removed outlier: 3.841A pdb=" N ILE C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 284 Processing helix chain 'C' and resid 294 through 297 No H-bonds generated for 'chain 'C' and resid 294 through 297' Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.586A pdb=" N ILE C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 315 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 404 removed outlier: 3.501A pdb=" N LEU C 397 " --> pdb=" O ASP C 393 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET C 402 " --> pdb=" O MET C 398 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 404 " --> pdb=" O THR C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 438 removed outlier: 3.735A pdb=" N LEU C 435 " --> pdb=" O MET C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 445 No H-bonds generated for 'chain 'C' and resid 443 through 445' Processing helix chain 'C' and resid 515 through 517 No H-bonds generated for 'chain 'C' and resid 515 through 517' Processing helix chain 'C' and resid 542 through 555 removed outlier: 3.581A pdb=" N LEU C 546 " --> pdb=" O PRO C 542 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 547 " --> pdb=" O GLU C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 565 removed outlier: 4.255A pdb=" N THR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.712A pdb=" N TYR C 572 " --> pdb=" O THR C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 582 Processing helix chain 'C' and resid 586 through 605 removed outlier: 3.540A pdb=" N ARG C 589 " --> pdb=" O LYS C 586 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA C 590 " --> pdb=" O GLY C 587 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 591 " --> pdb=" O ASN C 588 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY C 594 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG C 597 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN C 601 " --> pdb=" O THR C 598 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP C 605 " --> pdb=" O GLN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 621 removed outlier: 3.651A pdb=" N LYS C 617 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Proline residue: C 620 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 52 through 54 Processing sheet with id= B, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.204A pdb=" N TYR A 144 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLY A 121 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N HIS A 146 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR A 123 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE A 148 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 290 through 293 Processing sheet with id= D, first strand: chain 'A' and resid 477 through 479 removed outlier: 6.462A pdb=" N LEU A 558 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU A 539 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 560 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL A 537 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU A 539 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE A 322 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 614 through 619 removed outlier: 6.609A pdb=" N GLU A 624 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU A 618 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= G, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= H, first strand: chain 'B' and resid 178 through 192 Processing sheet with id= I, first strand: chain 'B' and resid 224 through 228 Processing sheet with id= J, first strand: chain 'B' and resid 483 through 486 Processing sheet with id= K, first strand: chain 'B' and resid 348 through 350 Processing sheet with id= L, first strand: chain 'B' and resid 355 through 359 Processing sheet with id= M, first strand: chain 'B' and resid 489 through 492 Processing sheet with id= N, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= O, first strand: chain 'C' and resid 133 through 135 Processing sheet with id= P, first strand: chain 'C' and resid 287 through 289 Processing sheet with id= Q, first strand: chain 'C' and resid 323 through 325 removed outlier: 3.636A pdb=" N PHE C 325 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 331 " --> pdb=" O ASN C 364 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLU C 362 " --> pdb=" O VAL C 333 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 342 through 345 Processing sheet with id= S, first strand: chain 'C' and resid 478 through 480 removed outlier: 7.961A pdb=" N ARG C 479 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA C 384 " --> pdb=" O ARG C 479 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS C 375 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA C 384 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL C 373 " --> pdb=" O ALA C 384 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 635 through 640 Processing sheet with id= U, first strand: chain 'C' and resid 657 through 659 Processing sheet with id= V, first strand: chain 'C' and resid 694 through 696 removed outlier: 3.500A pdb=" N LYS C 736 " --> pdb=" O GLU C 720 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLU C 720 " --> pdb=" O LYS C 736 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 141 through 148 removed outlier: 6.365A pdb=" N ARG C 214 " --> pdb=" O ILE C 147 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 6.46 Time building geometry restraints manager: 8.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3317 1.32 - 1.44: 4917 1.44 - 1.57: 10426 1.57 - 1.69: 85 1.69 - 1.81: 190 Bond restraints: 18935 Sorted by residual: bond pdb=" C19 M4H A 801 " pdb=" C20 M4H A 801 " ideal model delta sigma weight residual 1.414 1.462 -0.048 2.00e-02 2.50e+03 5.74e+00 bond pdb=" C1 M4H A 801 " pdb=" C6 M4H A 801 " ideal model delta sigma weight residual 1.437 1.477 -0.040 2.00e-02 2.50e+03 3.99e+00 bond pdb=" C13 M4H A 801 " pdb=" N18 M4H A 801 " ideal model delta sigma weight residual 1.459 1.498 -0.039 2.00e-02 2.50e+03 3.84e+00 bond pdb=" CG LEU B 337 " pdb=" CD1 LEU B 337 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.35e+00 bond pdb=" CB GLN A 476 " pdb=" CG GLN A 476 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.07e+00 ... (remaining 18930 not shown) Histogram of bond angle deviations from ideal: 98.70 - 106.87: 781 106.87 - 115.05: 11342 115.05 - 123.22: 12544 123.22 - 131.40: 1026 131.40 - 139.57: 54 Bond angle restraints: 25747 Sorted by residual: angle pdb=" C MET B 407 " pdb=" N MET B 408 " pdb=" CA MET B 408 " ideal model delta sigma weight residual 121.54 132.57 -11.03 1.91e+00 2.74e-01 3.34e+01 angle pdb=" N18 M4H A 801 " pdb=" C19 M4H A 801 " pdb=" N26 M4H A 801 " ideal model delta sigma weight residual 125.81 139.57 -13.76 3.00e+00 1.11e-01 2.10e+01 angle pdb=" N MET B 408 " pdb=" CA MET B 408 " pdb=" C MET B 408 " ideal model delta sigma weight residual 110.80 101.48 9.32 2.13e+00 2.20e-01 1.92e+01 angle pdb=" O4' A V 7 " pdb=" C1' A V 7 " pdb=" N9 A V 7 " ideal model delta sigma weight residual 108.20 113.54 -5.34 1.50e+00 4.44e-01 1.27e+01 angle pdb=" C2' A V 4 " pdb=" C1' A V 4 " pdb=" N9 A V 4 " ideal model delta sigma weight residual 112.00 117.12 -5.12 1.50e+00 4.44e-01 1.17e+01 ... (remaining 25742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10244 17.97 - 35.94: 971 35.94 - 53.91: 244 53.91 - 71.87: 106 71.87 - 89.84: 42 Dihedral angle restraints: 11607 sinusoidal: 5258 harmonic: 6349 Sorted by residual: dihedral pdb=" CA MET B 407 " pdb=" C MET B 407 " pdb=" N MET B 408 " pdb=" CA MET B 408 " ideal model delta harmonic sigma weight residual 180.00 150.00 30.00 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ILE A 481 " pdb=" C ILE A 481 " pdb=" N THR A 482 " pdb=" CA THR A 482 " ideal model delta harmonic sigma weight residual 180.00 153.18 26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA LEU A 219 " pdb=" C LEU A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 11604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1884 0.047 - 0.095: 778 0.095 - 0.142: 179 0.142 - 0.189: 23 0.189 - 0.236: 3 Chirality restraints: 2867 Sorted by residual: chirality pdb=" C1' A V 4 " pdb=" O4' A V 4 " pdb=" C2' A V 4 " pdb=" N9 A V 4 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C1' A V 7 " pdb=" O4' A V 7 " pdb=" C2' A V 7 " pdb=" N9 A V 7 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE B 392 " pdb=" CA ILE B 392 " pdb=" CG1 ILE B 392 " pdb=" CG2 ILE B 392 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2864 not shown) Planarity restraints: 3153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 7 " -0.038 2.00e-02 2.50e+03 1.77e-02 8.61e+00 pdb=" N9 A V 7 " 0.040 2.00e-02 2.50e+03 pdb=" C8 A V 7 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A V 7 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A V 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 7 " -0.014 2.00e-02 2.50e+03 pdb=" N6 A V 7 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A V 7 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A V 7 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A V 7 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A V 7 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 619 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO A 620 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 620 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 620 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " -0.037 2.00e-02 2.50e+03 1.66e-02 7.56e+00 pdb=" N9 A V 4 " 0.037 2.00e-02 2.50e+03 pdb=" C8 A V 4 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A V 4 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A V 4 " -0.008 2.00e-02 2.50e+03 pdb=" N6 A V 4 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A V 4 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A V 4 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A V 4 " 0.007 2.00e-02 2.50e+03 pdb=" C4 A V 4 " 0.004 2.00e-02 2.50e+03 ... (remaining 3150 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 286 2.60 - 3.17: 14361 3.17 - 3.75: 30590 3.75 - 4.32: 45231 4.32 - 4.90: 70610 Nonbonded interactions: 161078 Sorted by model distance: nonbonded pdb=" OD1 ASP A 108 " pdb="MG MG A 802 " model vdw 2.024 2.170 nonbonded pdb=" O11 M4H A 801 " pdb="MG MG A 803 " model vdw 2.035 2.170 nonbonded pdb=" OD1 ASP B 305 " pdb="MG MG B 801 " model vdw 2.036 2.170 nonbonded pdb=" OD2 ASP A 108 " pdb="MG MG A 803 " model vdw 2.055 2.170 nonbonded pdb=" OD1 ASP B 445 " pdb="MG MG B 801 " model vdw 2.059 2.170 ... (remaining 161073 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: 1.510 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: 0.020 Extract box with map and model: 7.700 Check model and map are aligned: 0.260 Set scattering table: 0.180 Process input model: 58.780 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.070 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:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.008 0.068 18935 Z= 0.512 Angle : 0.812 13.764 25747 Z= 0.451 Chirality : 0.052 0.236 2867 Planarity : 0.006 0.069 3153 Dihedral : 16.577 89.842 7503 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 5.99 % Allowed : 10.28 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -3.41 (0.14), residues: 2171 helix: -2.32 (0.12), residues: 972 sheet: -1.52 (0.31), residues: 241 loop : -2.26 (0.16), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 49 HIS 0.005 0.001 HIS C 437 PHE 0.029 0.003 PHE A 211 TYR 0.024 0.003 TYR B 557 ARG 0.005 0.001 ARG A 449 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 302 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5713 (tm-30) REVERT: A 82 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8233 (mm-40) REVERT: A 323 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8467 (pp) REVERT: A 374 MET cc_start: 0.7722 (ttm) cc_final: 0.7347 (tpp) REVERT: A 492 ARG cc_start: 0.7632 (ttm-80) cc_final: 0.7407 (ttp-170) REVERT: B 202 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7294 (tm-30) REVERT: B 227 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8197 (pmm) REVERT: B 296 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6877 (pt0) REVERT: B 384 ASP cc_start: 0.7767 (m-30) cc_final: 0.7494 (m-30) REVERT: B 619 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7434 (p0) REVERT: B 633 HIS cc_start: 0.8233 (t-90) cc_final: 0.7928 (t-90) REVERT: C 138 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: C 141 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8722 (p) REVERT: C 171 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: C 195 ASN cc_start: 0.6713 (m-40) cc_final: 0.6480 (m110) REVERT: C 392 GLU cc_start: 0.1944 (OUTLIER) cc_final: 0.1708 (tm-30) REVERT: C 394 ILE cc_start: 0.1343 (OUTLIER) cc_final: 0.0805 (mt) REVERT: C 395 LEU cc_start: 0.4315 (OUTLIER) cc_final: 0.4070 (tm) REVERT: C 431 MET cc_start: 0.5778 (mmm) cc_final: 0.5310 (mmm) REVERT: C 494 ILE cc_start: 0.4966 (OUTLIER) cc_final: 0.4623 (pt) REVERT: C 505 ARG cc_start: 0.5618 (OUTLIER) cc_final: 0.4562 (mtt90) REVERT: C 628 LEU cc_start: 0.5900 (OUTLIER) cc_final: 0.5664 (pt) REVERT: C 654 GLN cc_start: 0.7010 (pt0) cc_final: 0.6194 (mm110) REVERT: C 679 ILE cc_start: 0.2170 (OUTLIER) cc_final: 0.1589 (mt) outliers start: 116 outliers final: 42 residues processed: 388 average time/residue: 1.5928 time to fit residues: 681.5917 Evaluate side-chains 310 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 251 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 174 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 201 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 100 ASN A 239 ASN A 256 GLN A 476 GLN A 670 ASN A 691 ASN B 127 GLN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 ASN B 310 ASN B 372 ASN B 694 GLN B 745 ASN ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN C 563 GLN C 588 ASN C 602 GLN C 659 ASN C 663 ASN C 723 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18935 Z= 0.163 Angle : 0.490 8.425 25747 Z= 0.262 Chirality : 0.040 0.202 2867 Planarity : 0.004 0.051 3153 Dihedral : 12.973 89.715 3179 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.75 % Allowed : 15.86 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.16), residues: 2171 helix: -0.52 (0.15), residues: 967 sheet: -1.17 (0.33), residues: 237 loop : -1.79 (0.17), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 49 HIS 0.004 0.001 HIS C 551 PHE 0.015 0.001 PHE A 211 TYR 0.026 0.001 TYR B 557 ARG 0.008 0.000 ARG C 503 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 278 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4427 (OUTLIER) cc_final: 0.3991 (tmm) REVERT: A 42 MET cc_start: 0.7237 (tpp) cc_final: 0.6862 (tpt) REVERT: A 43 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6910 (tm-30) REVERT: A 147 ILE cc_start: 0.8480 (mm) cc_final: 0.8268 (mm) REVERT: A 374 MET cc_start: 0.7583 (ttm) cc_final: 0.7246 (tpp) REVERT: A 492 ARG cc_start: 0.7671 (ttm-80) cc_final: 0.7361 (ttm170) REVERT: B 171 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8798 (mp) REVERT: B 202 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7744 (tp40) REVERT: B 296 GLU cc_start: 0.7131 (pt0) cc_final: 0.6882 (pt0) REVERT: B 371 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7311 (pt0) REVERT: B 384 ASP cc_start: 0.7799 (m-30) cc_final: 0.7502 (m-30) REVERT: B 619 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7305 (p0) REVERT: B 633 HIS cc_start: 0.8179 (t-90) cc_final: 0.7932 (t-90) REVERT: B 704 THR cc_start: 0.8862 (p) cc_final: 0.8636 (m) REVERT: C 141 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8577 (t) REVERT: C 171 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.7810 (mm-30) REVERT: C 195 ASN cc_start: 0.6692 (m-40) cc_final: 0.6411 (m110) REVERT: C 431 MET cc_start: 0.5953 (mmm) cc_final: 0.5490 (mmm) REVERT: C 494 ILE cc_start: 0.4864 (OUTLIER) cc_final: 0.4659 (pt) REVERT: C 505 ARG cc_start: 0.5499 (OUTLIER) cc_final: 0.4474 (mtt90) REVERT: C 628 LEU cc_start: 0.5634 (OUTLIER) cc_final: 0.5316 (pt) REVERT: C 654 GLN cc_start: 0.7321 (pt0) cc_final: 0.6344 (mm110) outliers start: 92 outliers final: 42 residues processed: 343 average time/residue: 1.4884 time to fit residues: 566.1217 Evaluate side-chains 300 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 248 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 239 ASN A 670 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN B 694 GLN C 138 GLN C 233 HIS C 439 GLN C 551 HIS C 588 ASN C 663 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 18935 Z= 0.389 Angle : 0.593 8.077 25747 Z= 0.313 Chirality : 0.045 0.209 2867 Planarity : 0.005 0.047 3153 Dihedral : 12.603 90.143 3132 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.50 % Favored : 96.45 % Rotamer: Outliers : 5.73 % Allowed : 16.68 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2171 helix: -0.11 (0.16), residues: 971 sheet: -0.93 (0.32), residues: 250 loop : -1.69 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 557 HIS 0.004 0.001 HIS C 624 PHE 0.023 0.002 PHE A 211 TYR 0.026 0.002 TYR B 557 ARG 0.005 0.001 ARG B 560 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 243 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.7171 (tpp) cc_final: 0.6690 (tpt) REVERT: A 374 MET cc_start: 0.7741 (ttm) cc_final: 0.7454 (tpp) REVERT: A 492 ARG cc_start: 0.7667 (ttm-80) cc_final: 0.7394 (ttp-170) REVERT: B 187 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7224 (mttt) REVERT: B 192 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7677 (ttm170) REVERT: B 202 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: B 296 GLU cc_start: 0.7203 (pt0) cc_final: 0.6919 (pt0) REVERT: B 384 ASP cc_start: 0.7824 (m-30) cc_final: 0.7582 (m-30) REVERT: B 433 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7599 (mttm) REVERT: B 571 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7641 (mmp-170) REVERT: B 619 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7427 (p0) REVERT: B 633 HIS cc_start: 0.8261 (t-90) cc_final: 0.7900 (t-90) REVERT: B 656 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7195 (mt-10) REVERT: B 670 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7353 (mtt180) REVERT: B 672 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7344 (mtm-85) REVERT: C 141 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8630 (t) REVERT: C 171 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.7867 (mm-30) REVERT: C 195 ASN cc_start: 0.6824 (m-40) cc_final: 0.6496 (m110) REVERT: C 249 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5349 (mp0) REVERT: C 301 ASN cc_start: 0.5656 (OUTLIER) cc_final: 0.5285 (t0) REVERT: C 332 ARG cc_start: 0.5077 (OUTLIER) cc_final: 0.3773 (tmm-80) REVERT: C 394 ILE cc_start: 0.1912 (OUTLIER) cc_final: 0.1473 (mt) REVERT: C 494 ILE cc_start: 0.4899 (OUTLIER) cc_final: 0.4532 (pt) REVERT: C 505 ARG cc_start: 0.5590 (OUTLIER) cc_final: 0.4507 (mtt90) REVERT: C 654 GLN cc_start: 0.7315 (pt0) cc_final: 0.6352 (mm110) outliers start: 111 outliers final: 61 residues processed: 320 average time/residue: 1.4876 time to fit residues: 527.4191 Evaluate side-chains 316 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 239 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 192 ARG Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 209 ARG Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 672 ARG Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 4.9990 chunk 151 optimal weight: 0.0980 chunk 104 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 192 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 100 ASN A 239 ASN A 670 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 588 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18935 Z= 0.210 Angle : 0.502 7.440 25747 Z= 0.265 Chirality : 0.040 0.197 2867 Planarity : 0.004 0.045 3153 Dihedral : 12.300 89.526 3127 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.06 % Allowed : 17.51 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2171 helix: 0.33 (0.17), residues: 980 sheet: -0.79 (0.33), residues: 240 loop : -1.53 (0.18), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 49 HIS 0.004 0.001 HIS A 52 PHE 0.016 0.001 PHE A 211 TYR 0.023 0.001 TYR B 557 ARG 0.004 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 249 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 MET cc_start: 0.7153 (tpp) cc_final: 0.6639 (tpt) REVERT: A 100 ASN cc_start: 0.6758 (OUTLIER) cc_final: 0.6092 (m-40) REVERT: A 124 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.5742 (mtt180) REVERT: A 374 MET cc_start: 0.7702 (ttm) cc_final: 0.7362 (tpp) REVERT: A 395 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8163 (mmtt) REVERT: A 492 ARG cc_start: 0.7637 (ttm-80) cc_final: 0.7348 (ttp-170) REVERT: B 171 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8818 (mp) REVERT: B 202 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: B 296 GLU cc_start: 0.7141 (pt0) cc_final: 0.6882 (pt0) REVERT: B 384 ASP cc_start: 0.7806 (m-30) cc_final: 0.7543 (m-30) REVERT: B 619 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7336 (p0) REVERT: B 633 HIS cc_start: 0.8250 (t-90) cc_final: 0.7923 (t-90) REVERT: B 656 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7193 (mt-10) REVERT: B 670 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7327 (mtt180) REVERT: C 141 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8601 (t) REVERT: C 195 ASN cc_start: 0.6755 (m-40) cc_final: 0.6418 (m110) REVERT: C 249 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.5288 (mp0) REVERT: C 301 ASN cc_start: 0.5592 (OUTLIER) cc_final: 0.5257 (t0) REVERT: C 332 ARG cc_start: 0.4893 (OUTLIER) cc_final: 0.3731 (tmm-80) REVERT: C 354 MET cc_start: 0.4158 (OUTLIER) cc_final: 0.3734 (mmm) REVERT: C 429 ASN cc_start: 0.2538 (OUTLIER) cc_final: 0.1899 (m-40) REVERT: C 494 ILE cc_start: 0.4809 (OUTLIER) cc_final: 0.4503 (pt) REVERT: C 505 ARG cc_start: 0.5561 (OUTLIER) cc_final: 0.4489 (mtt90) REVERT: C 628 LEU cc_start: 0.5548 (OUTLIER) cc_final: 0.5192 (pt) outliers start: 98 outliers final: 51 residues processed: 317 average time/residue: 1.5251 time to fit residues: 535.7280 Evaluate side-chains 303 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 236 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 670 ARG Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 0.1980 chunk 192 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 239 ASN A 670 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN C 138 GLN C 160 GLN C 588 ASN C 639 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 18935 Z= 0.478 Angle : 0.640 9.879 25747 Z= 0.336 Chirality : 0.047 0.223 2867 Planarity : 0.005 0.047 3153 Dihedral : 12.519 90.209 3122 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.87 % Favored : 96.08 % Rotamer: Outliers : 6.04 % Allowed : 17.15 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2171 helix: 0.15 (0.16), residues: 976 sheet: -0.80 (0.32), residues: 250 loop : -1.59 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 49 HIS 0.005 0.001 HIS A 52 PHE 0.024 0.002 PHE A 211 TYR 0.025 0.002 TYR B 557 ARG 0.007 0.001 ARG B 429 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 245 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4625 (OUTLIER) cc_final: 0.3950 (tmm) REVERT: A 42 MET cc_start: 0.7173 (tpp) cc_final: 0.6684 (tpt) REVERT: A 124 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.6050 (mtt180) REVERT: A 374 MET cc_start: 0.7719 (ttm) cc_final: 0.7439 (tpp) REVERT: A 492 ARG cc_start: 0.7676 (ttm-80) cc_final: 0.7390 (ttp-170) REVERT: B 202 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: B 296 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6930 (pt0) REVERT: B 367 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: B 384 ASP cc_start: 0.7858 (m-30) cc_final: 0.7608 (m-30) REVERT: B 571 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7651 (mmp-170) REVERT: B 619 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7451 (p0) REVERT: B 633 HIS cc_start: 0.8294 (t-90) cc_final: 0.7926 (t-90) REVERT: B 656 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7228 (mt-10) REVERT: B 724 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8257 (tp) REVERT: C 6 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: C 171 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: C 195 ASN cc_start: 0.6835 (m-40) cc_final: 0.6478 (m110) REVERT: C 210 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7409 (tp30) REVERT: C 249 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5414 (mp0) REVERT: C 301 ASN cc_start: 0.5669 (OUTLIER) cc_final: 0.5287 (t0) REVERT: C 332 ARG cc_start: 0.5290 (OUTLIER) cc_final: 0.4026 (tmm-80) REVERT: C 354 MET cc_start: 0.4249 (OUTLIER) cc_final: 0.3821 (mmm) REVERT: C 394 ILE cc_start: 0.1753 (OUTLIER) cc_final: 0.1311 (mt) REVERT: C 429 ASN cc_start: 0.2665 (OUTLIER) cc_final: 0.1936 (m110) REVERT: C 464 MET cc_start: 0.1588 (mmm) cc_final: -0.0245 (tpp) REVERT: C 494 ILE cc_start: 0.4917 (OUTLIER) cc_final: 0.4592 (pt) REVERT: C 505 ARG cc_start: 0.5621 (OUTLIER) cc_final: 0.4510 (mtt90) REVERT: C 628 LEU cc_start: 0.5779 (OUTLIER) cc_final: 0.5401 (pt) outliers start: 117 outliers final: 63 residues processed: 326 average time/residue: 1.4951 time to fit residues: 540.7560 Evaluate side-chains 312 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 229 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 367 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 243 GLN Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 437 HIS Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 505 ARG Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 684 SER Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 732 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 0.0170 chunk 193 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 214 optimal weight: 0.0070 chunk 178 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 239 ASN A 494 ASN A 670 ASN B 65 GLN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18935 Z= 0.116 Angle : 0.457 7.791 25747 Z= 0.241 Chirality : 0.038 0.190 2867 Planarity : 0.003 0.043 3153 Dihedral : 12.026 88.729 3121 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.93 % Allowed : 20.14 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.47 (0.18), residues: 2171 helix: 0.76 (0.17), residues: 972 sheet: -0.66 (0.33), residues: 238 loop : -1.32 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 49 HIS 0.004 0.001 HIS A 52 PHE 0.011 0.001 PHE C 694 TYR 0.020 0.001 TYR B 557 ARG 0.006 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 256 time to evaluate : 2.164 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 1 MET cc_start: 0.4397 (OUTLIER) cc_final: 0.3911 (tmm) REVERT: A 42 MET cc_start: 0.7149 (tpp) cc_final: 0.6626 (tpt) REVERT: A 374 MET cc_start: 0.7683 (ttm) cc_final: 0.7308 (tpp) REVERT: A 492 ARG cc_start: 0.7597 (ttm-80) cc_final: 0.7308 (ttp-170) REVERT: B 60 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7715 (mp0) REVERT: B 171 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8814 (mp) REVERT: B 202 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7704 (tp-100) REVERT: B 296 GLU cc_start: 0.7089 (pt0) cc_final: 0.6839 (pt0) REVERT: B 384 ASP cc_start: 0.7835 (m-30) cc_final: 0.7556 (m-30) REVERT: B 619 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7359 (p0) REVERT: B 633 HIS cc_start: 0.8214 (t-90) cc_final: 0.7927 (t-90) REVERT: B 656 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7228 (mt-10) REVERT: C 6 GLU cc_start: 0.8026 (tt0) cc_final: 0.7790 (tt0) REVERT: C 301 ASN cc_start: 0.5529 (OUTLIER) cc_final: 0.5224 (t0) REVERT: C 354 MET cc_start: 0.4043 (OUTLIER) cc_final: 0.3760 (mmm) REVERT: C 394 ILE cc_start: 0.1823 (OUTLIER) cc_final: 0.1305 (mt) REVERT: C 429 ASN cc_start: 0.2584 (OUTLIER) cc_final: 0.1954 (m-40) REVERT: C 494 ILE cc_start: 0.4924 (OUTLIER) cc_final: 0.4594 (pt) REVERT: C 586 LYS cc_start: 0.7426 (mtpt) cc_final: 0.7000 (tptm) outliers start: 76 outliers final: 37 residues processed: 307 average time/residue: 1.5126 time to fit residues: 514.2644 Evaluate side-chains 279 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 233 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 156 optimal weight: 0.2980 chunk 121 optimal weight: 9.9990 chunk 180 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 HIS A 670 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18935 Z= 0.209 Angle : 0.495 10.184 25747 Z= 0.260 Chirality : 0.040 0.182 2867 Planarity : 0.004 0.044 3153 Dihedral : 11.955 88.755 3109 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.03 % Allowed : 20.61 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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 (0.18), residues: 2171 helix: 0.83 (0.17), residues: 975 sheet: -0.55 (0.33), residues: 248 loop : -1.29 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 49 HIS 0.004 0.001 HIS A 52 PHE 0.017 0.001 PHE A 211 TYR 0.022 0.001 TYR B 557 ARG 0.005 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 237 time to evaluate : 2.086 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: A 1 MET cc_start: 0.4379 (OUTLIER) cc_final: 0.3826 (tmm) REVERT: A 42 MET cc_start: 0.7168 (tpp) cc_final: 0.6597 (tpt) REVERT: A 374 MET cc_start: 0.7693 (ttm) cc_final: 0.7313 (tpp) REVERT: A 492 ARG cc_start: 0.7633 (ttm-80) cc_final: 0.7358 (ttp-170) REVERT: B 171 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8831 (mp) REVERT: B 202 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: B 296 GLU cc_start: 0.7129 (pt0) cc_final: 0.6865 (pt0) REVERT: B 371 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7396 (pt0) REVERT: B 384 ASP cc_start: 0.7820 (m-30) cc_final: 0.7569 (m-30) REVERT: B 619 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7337 (p0) REVERT: B 633 HIS cc_start: 0.8249 (t-90) cc_final: 0.7916 (t-90) REVERT: B 656 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7244 (mt-10) REVERT: C 171 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.7711 (mm-30) REVERT: C 301 ASN cc_start: 0.5627 (OUTLIER) cc_final: 0.5239 (t0) REVERT: C 332 ARG cc_start: 0.4914 (OUTLIER) cc_final: 0.3797 (tmm-80) REVERT: C 394 ILE cc_start: 0.1746 (OUTLIER) cc_final: 0.1203 (mt) REVERT: C 429 ASN cc_start: 0.2520 (OUTLIER) cc_final: 0.1883 (m-40) REVERT: C 494 ILE cc_start: 0.4722 (OUTLIER) cc_final: 0.4518 (pt) REVERT: C 586 LYS cc_start: 0.7441 (mtpt) cc_final: 0.7022 (tptm) outliers start: 78 outliers final: 41 residues processed: 291 average time/residue: 1.4749 time to fit residues: 476.5951 Evaluate side-chains 284 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 232 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 670 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18935 Z= 0.173 Angle : 0.479 10.569 25747 Z= 0.251 Chirality : 0.039 0.180 2867 Planarity : 0.004 0.066 3153 Dihedral : 11.877 88.545 3109 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.87 % Allowed : 20.97 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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 (0.18), residues: 2171 helix: 0.93 (0.17), residues: 982 sheet: -0.45 (0.33), residues: 248 loop : -1.21 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 49 HIS 0.004 0.001 HIS A 52 PHE 0.015 0.001 PHE A 211 TYR 0.021 0.001 TYR B 557 ARG 0.006 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 243 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4428 (OUTLIER) cc_final: 0.3901 (tmm) REVERT: A 10 ASN cc_start: 0.5888 (OUTLIER) cc_final: 0.5459 (t0) REVERT: A 42 MET cc_start: 0.7171 (tpp) cc_final: 0.6639 (tpt) REVERT: A 374 MET cc_start: 0.7632 (ttm) cc_final: 0.7239 (tpp) REVERT: A 492 ARG cc_start: 0.7625 (ttm-80) cc_final: 0.7353 (ttp-170) REVERT: B 171 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8840 (mp) REVERT: B 202 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7723 (tp-100) REVERT: B 296 GLU cc_start: 0.7116 (pt0) cc_final: 0.6842 (pt0) REVERT: B 371 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7372 (pt0) REVERT: B 384 ASP cc_start: 0.7823 (m-30) cc_final: 0.7577 (m-30) REVERT: B 619 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7377 (p0) REVERT: B 633 HIS cc_start: 0.8246 (t-90) cc_final: 0.7913 (t-90) REVERT: B 656 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7225 (mt-10) REVERT: C 6 GLU cc_start: 0.8052 (tt0) cc_final: 0.7800 (tt0) REVERT: C 249 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.5363 (mp0) REVERT: C 277 LEU cc_start: 0.6336 (tp) cc_final: 0.6087 (tp) REVERT: C 301 ASN cc_start: 0.5577 (OUTLIER) cc_final: 0.5216 (t0) REVERT: C 394 ILE cc_start: 0.1700 (OUTLIER) cc_final: 0.1167 (mt) REVERT: C 429 ASN cc_start: 0.2504 (OUTLIER) cc_final: 0.1873 (m-40) REVERT: C 452 GLU cc_start: 0.2408 (OUTLIER) cc_final: 0.1881 (tm-30) REVERT: C 586 LYS cc_start: 0.7416 (mtpt) cc_final: 0.7009 (tptm) outliers start: 75 outliers final: 44 residues processed: 297 average time/residue: 1.6416 time to fit residues: 539.6630 Evaluate side-chains 289 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 234 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 202 GLN Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 410 MET Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 6.9990 chunk 204 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 156 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 180 optimal weight: 30.0000 chunk 188 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 670 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 18935 Z= 0.439 Angle : 0.620 12.635 25747 Z= 0.325 Chirality : 0.046 0.218 2867 Planarity : 0.005 0.062 3153 Dihedral : 12.176 89.870 3105 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.59 % Favored : 96.36 % Rotamer: Outliers : 3.87 % Allowed : 21.07 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.68 (0.17), residues: 2171 helix: 0.50 (0.16), residues: 989 sheet: -0.54 (0.32), residues: 250 loop : -1.44 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 438 HIS 0.006 0.001 HIS A 52 PHE 0.024 0.002 PHE A 211 TYR 0.025 0.002 TYR A 131 ARG 0.008 0.001 ARG B 429 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 235 time to evaluate : 2.200 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: A 1 MET cc_start: 0.4500 (OUTLIER) cc_final: 0.3867 (tmm) REVERT: A 10 ASN cc_start: 0.5952 (OUTLIER) cc_final: 0.5559 (t0) REVERT: A 42 MET cc_start: 0.7164 (tpp) cc_final: 0.6675 (tpt) REVERT: A 374 MET cc_start: 0.7756 (ttm) cc_final: 0.7407 (tpp) REVERT: A 492 ARG cc_start: 0.7665 (ttm-80) cc_final: 0.7389 (ttp-170) REVERT: B 296 GLU cc_start: 0.7180 (pt0) cc_final: 0.6932 (pt0) REVERT: B 371 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7467 (pt0) REVERT: B 384 ASP cc_start: 0.7850 (m-30) cc_final: 0.7640 (m-30) REVERT: B 571 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7635 (mmp-170) REVERT: B 619 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7423 (p0) REVERT: B 633 HIS cc_start: 0.8292 (t-90) cc_final: 0.7913 (t-90) REVERT: B 656 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7192 (mt-10) REVERT: C 249 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.5403 (mp0) REVERT: C 301 ASN cc_start: 0.5685 (OUTLIER) cc_final: 0.5288 (t0) REVERT: C 332 ARG cc_start: 0.5241 (OUTLIER) cc_final: 0.3961 (tmm-80) REVERT: C 394 ILE cc_start: 0.1840 (OUTLIER) cc_final: 0.1325 (mt) REVERT: C 429 ASN cc_start: 0.2701 (OUTLIER) cc_final: 0.2057 (m-40) REVERT: C 452 GLU cc_start: 0.2640 (OUTLIER) cc_final: 0.1968 (tm-30) outliers start: 75 outliers final: 48 residues processed: 291 average time/residue: 1.5295 time to fit residues: 492.9036 Evaluate side-chains 289 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 230 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 670 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18935 Z= 0.287 Angle : 0.554 12.287 25747 Z= 0.291 Chirality : 0.042 0.204 2867 Planarity : 0.004 0.057 3153 Dihedral : 11.987 89.725 3102 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.68 % Rotamer: Outliers : 3.72 % Allowed : 21.33 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -0.57 (0.17), residues: 2171 helix: 0.62 (0.17), residues: 983 sheet: -0.53 (0.33), residues: 246 loop : -1.38 (0.18), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 49 HIS 0.005 0.001 HIS A 52 PHE 0.019 0.002 PHE A 211 TYR 0.025 0.002 TYR A 130 ARG 0.007 0.000 ARG B 429 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4342 Ramachandran restraints generated. 2171 Oldfield, 0 Emsley, 2171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 234 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4450 (OUTLIER) cc_final: 0.3799 (tmm) REVERT: A 10 ASN cc_start: 0.5980 (OUTLIER) cc_final: 0.5580 (t0) REVERT: A 42 MET cc_start: 0.7159 (tpp) cc_final: 0.6572 (tpt) REVERT: A 374 MET cc_start: 0.7755 (ttm) cc_final: 0.7406 (tpp) REVERT: A 492 ARG cc_start: 0.7648 (ttm-80) cc_final: 0.7347 (ttp-170) REVERT: B 296 GLU cc_start: 0.7126 (pt0) cc_final: 0.6870 (pt0) REVERT: B 371 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7438 (pt0) REVERT: B 384 ASP cc_start: 0.7839 (m-30) cc_final: 0.7613 (m-30) REVERT: B 619 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.7378 (p0) REVERT: B 633 HIS cc_start: 0.8278 (t-90) cc_final: 0.7933 (t-90) REVERT: B 656 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7203 (mt-10) REVERT: C 210 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7529 (tp30) REVERT: C 249 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.5404 (mp0) REVERT: C 301 ASN cc_start: 0.5674 (OUTLIER) cc_final: 0.5272 (t0) REVERT: C 332 ARG cc_start: 0.5150 (OUTLIER) cc_final: 0.3878 (tmm-80) REVERT: C 394 ILE cc_start: 0.1672 (OUTLIER) cc_final: 0.1466 (mt) REVERT: C 429 ASN cc_start: 0.2613 (OUTLIER) cc_final: 0.1976 (m-40) REVERT: C 452 GLU cc_start: 0.2577 (OUTLIER) cc_final: 0.1919 (tm-30) outliers start: 72 outliers final: 48 residues processed: 291 average time/residue: 1.5283 time to fit residues: 493.4180 Evaluate side-chains 288 residues out of total 1936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 229 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 687 ARG Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 452 GLU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 562 THR Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 731 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 3.9990 chunk 187 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 181 optimal weight: 40.0000 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 670 ASN ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN C 138 GLN ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.164270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.123578 restraints weight = 19866.678| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.42 r_work: 0.3071 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18935 Z= 0.241 Angle : 0.531 11.179 25747 Z= 0.278 Chirality : 0.041 0.197 2867 Planarity : 0.004 0.055 3153 Dihedral : 11.918 89.360 3102 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 3.67 % Allowed : 21.28 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.17), residues: 2171 helix: 0.77 (0.17), residues: 975 sheet: -0.43 (0.34), residues: 239 loop : -1.34 (0.18), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 49 HIS 0.005 0.001 HIS A 52 PHE 0.018 0.002 PHE A 148 TYR 0.022 0.002 TYR A 131 ARG 0.006 0.000 ARG B 429 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8298.66 seconds wall clock time: 147 minutes 57.67 seconds (8877.67 seconds total)