Starting phenix.real_space_refine on Sun Mar 17 08:22:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9g_27261/03_2024/8d9g_27261.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9g_27261/03_2024/8d9g_27261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9g_27261/03_2024/8d9g_27261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9g_27261/03_2024/8d9g_27261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9g_27261/03_2024/8d9g_27261.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9g_27261/03_2024/8d9g_27261.pdb" } resolution = 2.57 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= 0.055 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 Zn 4 6.06 5 P 59 5.49 5 S 57 5.16 5 C 10676 2.51 5 N 2981 2.21 5 O 3371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 18": "OD1" <-> "OD2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 475": "OD1" <-> "OD2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A ASP 534": "OD1" <-> "OD2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B ASP 161": "OD1" <-> "OD2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B ASP 266": "OD1" <-> "OD2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "B PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 438": "OE1" <-> "OE2" Residue "B TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 521": "OE1" <-> "OE2" Residue "B ASP 537": "OD1" <-> "OD2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B GLU 565": "OE1" <-> "OE2" Residue "B GLU 576": "OE1" <-> "OE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B ASP 639": "OD1" <-> "OD2" Residue "B GLU 666": "OE1" <-> "OE2" Residue "B GLU 688": "OE1" <-> "OE2" Residue "B ASP 704": "OD1" <-> "OD2" Residue "B GLU 710": "OE1" <-> "OE2" Residue "B GLU 740": "OE1" <-> "OE2" Residue "B ASP 741": "OD1" <-> "OD2" Residue "B GLU 765": "OE1" <-> "OE2" Residue "B GLU 776": "OE1" <-> "OE2" Residue "B GLU 779": "OE1" <-> "OE2" Residue "B ASP 869": "OD1" <-> "OD2" Residue "B ASP 909": "OD1" <-> "OD2" Residue "B PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 923": "OD1" <-> "OD2" Residue "B GLU 942": "OE1" <-> "OE2" Residue "B ASP 966": "OD1" <-> "OD2" Residue "B GLU 1007": "OE1" <-> "OE2" Residue "B ARG 1441": "NH1" <-> "NH2" Residue "B GLU 1446": "OE1" <-> "OE2" Residue "B ARG 1458": "NH1" <-> "NH2" Residue "B ASP 1465": "OD1" <-> "OD2" Residue "B GLU 1469": "OE1" <-> "OE2" Residue "B TYR 1476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1491": "OE1" <-> "OE2" Residue "B GLU 1494": "OE1" <-> "OE2" Residue "B GLU 1505": "OE1" <-> "OE2" Residue "B ARG 1518": "NH1" <-> "NH2" Residue "B GLU 1524": "OE1" <-> "OE2" Residue "B ASP 1560": "OD1" <-> "OD2" Residue "B ASP 1572": "OD1" <-> "OD2" Residue "B ASP 1581": "OD1" <-> "OD2" Residue "B GLU 1595": "OE1" <-> "OE2" Residue "B GLU 1635": "OE1" <-> "OE2" Residue "B GLU 1652": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17148 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5516 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 658} Chain breaks: 1 Chain: "B" Number of atoms: 10373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1286, 10373 Classifications: {'peptide': 1286} Link IDs: {'PTRANS': 59, 'TRANS': 1226} Chain breaks: 3 Chain: "C" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 757 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 5, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 15} Chain: "D" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 498 Classifications: {'RNA': 23} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 19} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6184 SG CYS B 83 55.509 70.014 21.893 1.00 70.17 S ATOM 6455 SG CYS B 116 56.901 72.883 21.151 1.00 87.17 S ATOM 6501 SG CYS B 122 54.473 74.020 23.376 1.00 69.96 S ATOM 6525 SG CYS B 125 58.265 71.375 24.386 1.00 57.55 S ATOM 9248 SG CYS B 486 47.866 48.591 48.967 1.00 45.05 S ATOM 9316 SG CYS B 496 48.333 49.220 45.654 1.00 40.89 S ATOM 9330 SG CYS B 498 44.875 48.538 47.463 1.00 42.52 S ATOM 9352 SG CYS B 501 48.213 52.200 48.185 1.00 37.30 S ATOM 11336 SG CYS B 747 48.333 32.100 75.440 1.00 55.21 S ATOM 13333 SG CYS B1013 59.273 32.549 110.818 1.00 65.16 S ATOM 13543 SG CYS B1401 59.920 30.605 107.976 1.00 68.33 S ATOM 13594 SG CYS B1409 56.903 30.269 109.626 1.00 59.43 S ATOM 13611 SG CYS B1412 57.239 33.708 108.067 1.00 55.42 S Time building chain proxies: 9.00, per 1000 atoms: 0.52 Number of scatterers: 17148 At special positions: 0 Unit cell: (105.93, 100.58, 162.64, 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) Zn 4 29.99 S 57 16.00 P 59 15.00 O 3371 8.00 N 2981 7.00 C 10676 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: 7.12 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1701 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 125 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 116 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 83 " pdb="ZN ZN B1701 " - pdb=" SG CYS B 122 " pdb=" ZN B1702 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 501 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 496 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 486 " pdb="ZN ZN B1702 " - pdb=" SG CYS B 498 " pdb=" ZN B1703 " pdb="ZN ZN B1703 " - pdb=" ND1 HIS B 742 " pdb="ZN ZN B1703 " - pdb=" SG CYS B 747 " pdb=" ZN B1704 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1409 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1401 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1013 " pdb="ZN ZN B1704 " - pdb=" SG CYS B1412 " Number of angles added : 18 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3644 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 22 sheets defined 40.5% alpha, 18.5% beta 14 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 5.92 Creating SS restraints... Processing helix chain 'A' and resid 15 through 33 Processing helix chain 'A' and resid 39 through 59 removed outlier: 4.292A pdb=" N LYS A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 81 removed outlier: 3.700A pdb=" N THR A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.701A pdb=" N LYS A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 136 Processing helix chain 'A' and resid 141 through 155 removed outlier: 3.514A pdb=" N LEU A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 Processing helix chain 'A' and resid 180 through 190 removed outlier: 4.539A pdb=" N ASP A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASN A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 208 through 223 Processing helix chain 'A' and resid 230 through 247 removed outlier: 4.337A pdb=" N ASP A 234 " --> pdb=" O HIS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.559A pdb=" N ASP A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 339 through 357 removed outlier: 3.965A pdb=" N HIS A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 450 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 454 through 469 Processing helix chain 'A' and resid 470 through 474 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 509 through 514 removed outlier: 3.966A pdb=" N ASN A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 552 removed outlier: 3.701A pdb=" N ASN A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.645A pdb=" N THR A 669 " --> pdb=" O ARG A 665 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 679 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 691 removed outlier: 4.190A pdb=" N TRP A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.761A pdb=" N PHE A 703 " --> pdb=" O HIS A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 26 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 54 through 72 Processing helix chain 'B' and resid 122 through 128 Processing helix chain 'B' and resid 164 through 167 No H-bonds generated for 'chain 'B' and resid 164 through 167' Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.596A pdb=" N ALA B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 282 removed outlier: 3.554A pdb=" N ASN B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 removed outlier: 4.093A pdb=" N ILE B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 302 removed outlier: 4.502A pdb=" N GLY B 302 " --> pdb=" O ARG B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 303 through 308 Processing helix chain 'B' and resid 333 through 345 Processing helix chain 'B' and resid 349 through 369 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 466 through 483 Processing helix chain 'B' and resid 498 through 505 Processing helix chain 'B' and resid 564 through 574 Processing helix chain 'B' and resid 612 through 620 Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 625 through 631 Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 649 through 652 Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 682 through 688 Processing helix chain 'B' and resid 718 through 735 Processing helix chain 'B' and resid 749 through 754 Processing helix chain 'B' and resid 771 through 775 Processing helix chain 'B' and resid 826 through 842 Processing helix chain 'B' and resid 850 through 854 Processing helix chain 'B' and resid 868 through 878 removed outlier: 3.801A pdb=" N THR B 878 " --> pdb=" O MET B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1011 removed outlier: 3.702A pdb=" N LEU B 998 " --> pdb=" O PRO B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1389 through 1394 Processing helix chain 'B' and resid 1395 through 1399 Processing helix chain 'B' and resid 1409 through 1415 Processing helix chain 'B' and resid 1481 through 1488 removed outlier: 3.722A pdb=" N ILE B1485 " --> pdb=" O GLY B1481 " (cutoff:3.500A) Processing helix chain 'B' and resid 1488 through 1496 Processing helix chain 'B' and resid 1523 through 1535 Processing helix chain 'B' and resid 1547 through 1551 Processing helix chain 'B' and resid 1578 through 1598 removed outlier: 3.770A pdb=" N GLY B1598 " --> pdb=" O ILE B1594 " (cutoff:3.500A) Processing helix chain 'B' and resid 1610 through 1613 removed outlier: 3.727A pdb=" N VAL B1613 " --> pdb=" O GLN B1610 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1610 through 1613' Processing helix chain 'B' and resid 1614 through 1624 Processing helix chain 'B' and resid 1668 through 1678 Processing sheet with id=AA1, first strand: chain 'A' and resid 425 through 431 removed outlier: 6.629A pdb=" N VAL A 401 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 487 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 403 " --> pdb=" O VAL A 487 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 540 removed outlier: 7.080A pdb=" N VAL A 537 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU A 583 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 539 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A 580 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY A 625 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 582 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR A 660 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.529A pdb=" N SER B 51 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG B 14 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N TRP B 39 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL B 16 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N TRP B 41 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP B 190 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N GLU B 17 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 13.336A pdb=" N ARG B 188 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP B 185 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 162 through 163 removed outlier: 3.915A pdb=" N LEU B 162 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER B 51 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AA6, first strand: chain 'B' and resid 105 through 106 removed outlier: 6.034A pdb=" N THR B 105 " --> pdb=" O VAL B 400 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 374 through 375 Processing sheet with id=AA8, first strand: chain 'B' and resid 507 through 509 removed outlier: 6.533A pdb=" N GLU B 410 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU B 606 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 412 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE B 604 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 414 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE B 602 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 507 through 509 removed outlier: 6.533A pdb=" N GLU B 410 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU B 606 " --> pdb=" O GLU B 410 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 412 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE B 604 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 414 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE B 602 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 426 through 427 removed outlier: 4.182A pdb=" N ASN B 454 " --> pdb=" O VAL B 427 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 464 through 465 Processing sheet with id=AB3, first strand: chain 'B' and resid 521 through 528 removed outlier: 10.144A pdb=" N GLU B 521 " --> pdb=" O ASP B 542 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ASP B 542 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 11.103A pdb=" N ARG B 523 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 9.851A pdb=" N LEU B 540 " --> pdb=" O ARG B 523 " (cutoff:3.500A) removed outlier: 10.435A pdb=" N ARG B 525 " --> pdb=" O GLY B 538 " (cutoff:3.500A) removed outlier: 9.557A pdb=" N GLY B 538 " --> pdb=" O ARG B 525 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA B 527 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 698 through 699 removed outlier: 5.791A pdb=" N PHE B 715 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 698 through 699 removed outlier: 5.791A pdb=" N PHE B 715 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLN B 668 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE B 863 " --> pdb=" O GLN B 668 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 670 " --> pdb=" O ILE B 861 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE B 861 " --> pdb=" O THR B 670 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU B 672 " --> pdb=" O ALA B 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 680 through 681 removed outlier: 3.626A pdb=" N ILE B 695 " --> pdb=" O ASP B 681 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AB8, first strand: chain 'B' and resid 782 through 787 removed outlier: 6.020A pdb=" N ALA B 798 " --> pdb=" O ALA B 786 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 915 through 916 Processing sheet with id=AC1, first strand: chain 'B' and resid 919 through 922 Processing sheet with id=AC2, first strand: chain 'B' and resid 986 through 987 removed outlier: 6.614A pdb=" N LEU B 991 " --> pdb=" O TYR B1431 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA B1429 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ASP B1516 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N TYR B1431 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER B1514 " --> pdb=" O TYR B1431 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN B1433 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B1512 " --> pdb=" O THR B 955 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR B 955 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SER B1514 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 953 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP B1516 " --> pdb=" O CYS B 951 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N CYS B 951 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG B1518 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE B 949 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLU B1520 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY B 947 " --> pdb=" O GLU B1520 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER B 946 " --> pdb=" O THR B1564 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B1564 " --> pdb=" O SER B 946 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B 948 " --> pdb=" O LEU B1562 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B1562 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASN B 950 " --> pdb=" O ASP B1560 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1424 through 1426 removed outlier: 6.862A pdb=" N VAL B1512 " --> pdb=" O THR B 955 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR B 955 " --> pdb=" O VAL B1512 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SER B1514 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 953 " --> pdb=" O SER B1514 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP B1516 " --> pdb=" O CYS B 951 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N CYS B 951 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG B1518 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE B 949 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLU B1520 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY B 947 " --> pdb=" O GLU B1520 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER B 946 " --> pdb=" O THR B1564 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B1564 " --> pdb=" O SER B 946 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS B 948 " --> pdb=" O LEU B1562 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B1562 " --> pdb=" O LYS B 948 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASN B 950 " --> pdb=" O ASP B1560 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 980 through 982 removed outlier: 6.197A pdb=" N LYS B 980 " --> pdb=" O THR B1503 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N GLU B1505 " --> pdb=" O LYS B 980 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N TYR B 982 " --> pdb=" O GLU B1505 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 6.87 Time building geometry restraints manager: 7.71 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: 3379 1.32 - 1.45: 4563 1.45 - 1.57: 9514 1.57 - 1.69: 116 1.69 - 1.82: 80 Bond restraints: 17652 Sorted by residual: bond pdb=" CA ASN B 73 " pdb=" C ASN B 73 " ideal model delta sigma weight residual 1.523 1.494 0.030 1.56e-02 4.11e+03 3.62e+00 bond pdb=" C PHE A 714 " pdb=" N PRO A 715 " ideal model delta sigma weight residual 1.335 1.319 0.016 8.70e-03 1.32e+04 3.29e+00 bond pdb=" CD1 TYR B 365 " pdb=" CE1 TYR B 365 " ideal model delta sigma weight residual 1.382 1.331 0.051 3.00e-02 1.11e+03 2.90e+00 bond pdb=" CD1 TYR B 558 " pdb=" CE1 TYR B 558 " ideal model delta sigma weight residual 1.382 1.331 0.051 3.00e-02 1.11e+03 2.86e+00 bond pdb=" CB LEU A 598 " pdb=" CG LEU A 598 " ideal model delta sigma weight residual 1.530 1.563 -0.033 2.00e-02 2.50e+03 2.77e+00 ... (remaining 17647 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.73: 572 105.73 - 112.84: 9483 112.84 - 119.95: 6212 119.95 - 127.06: 7476 127.06 - 134.17: 342 Bond angle restraints: 24085 Sorted by residual: angle pdb=" C PRO A 335 " pdb=" N LYS A 336 " pdb=" CA LYS A 336 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" O4' G C 40 " pdb=" C1' G C 40 " pdb=" N9 G C 40 " ideal model delta sigma weight residual 108.20 114.22 -6.02 1.50e+00 4.44e-01 1.61e+01 angle pdb=" O4' A C 28 " pdb=" C1' A C 28 " pdb=" N9 A C 28 " ideal model delta sigma weight residual 108.20 114.05 -5.85 1.50e+00 4.44e-01 1.52e+01 angle pdb=" N GLU B1436 " pdb=" CA GLU B1436 " pdb=" CB GLU B1436 " ideal model delta sigma weight residual 114.17 109.80 4.37 1.14e+00 7.69e-01 1.47e+01 angle pdb=" N GLN B 34 " pdb=" CA GLN B 34 " pdb=" C GLN B 34 " ideal model delta sigma weight residual 111.75 116.56 -4.81 1.28e+00 6.10e-01 1.41e+01 ... (remaining 24080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 10201 35.32 - 70.64: 446 70.64 - 105.95: 42 105.95 - 141.27: 1 141.27 - 176.59: 5 Dihedral angle restraints: 10695 sinusoidal: 5026 harmonic: 5669 Sorted by residual: dihedral pdb=" O4' C C 22 " pdb=" C1' C C 22 " pdb=" N1 C C 22 " pdb=" C2 C C 22 " ideal model delta sinusoidal sigma weight residual 200.00 23.97 176.03 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C D 21 " pdb=" C1' C D 21 " pdb=" N1 C D 21 " pdb=" C2 C D 21 " ideal model delta sinusoidal sigma weight residual -160.00 -11.80 -148.20 1 1.50e+01 4.44e-03 7.89e+01 dihedral pdb=" O4' U C 15 " pdb=" C1' U C 15 " pdb=" N1 U C 15 " pdb=" C2 U C 15 " ideal model delta sinusoidal sigma weight residual 232.00 55.41 176.59 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 10692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2062 0.061 - 0.121: 491 0.121 - 0.182: 59 0.182 - 0.243: 6 0.243 - 0.303: 2 Chirality restraints: 2620 Sorted by residual: chirality pdb=" C1' A C 28 " pdb=" O4' A C 28 " pdb=" C2' A C 28 " pdb=" N9 A C 28 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C1' G C 40 " pdb=" O4' G C 40 " pdb=" C2' G C 40 " pdb=" N9 G C 40 " both_signs ideal model delta sigma weight residual False 2.44 2.15 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1' C D 38 " pdb=" O4' C D 38 " pdb=" C2' C D 38 " pdb=" N1 C D 38 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2617 not shown) Planarity restraints: 2884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 38 " 0.045 2.00e-02 2.50e+03 2.29e-02 1.18e+01 pdb=" N1 C C 38 " -0.048 2.00e-02 2.50e+03 pdb=" C2 C C 38 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C C 38 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C C 38 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C C 38 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C C 38 " 0.015 2.00e-02 2.50e+03 pdb=" C5 C C 38 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C C 38 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 28 " 0.033 2.00e-02 2.50e+03 1.73e-02 8.26e+00 pdb=" N9 A C 28 " -0.045 2.00e-02 2.50e+03 pdb=" C8 A C 28 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A C 28 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A C 28 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A C 28 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A C 28 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A C 28 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A C 28 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A C 28 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A C 28 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 40 " 0.033 2.00e-02 2.50e+03 1.63e-02 7.94e+00 pdb=" N9 G C 40 " -0.044 2.00e-02 2.50e+03 pdb=" C8 G C 40 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G C 40 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G C 40 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G C 40 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G C 40 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G C 40 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G C 40 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G C 40 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G C 40 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G C 40 " -0.006 2.00e-02 2.50e+03 ... (remaining 2881 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 241 2.61 - 3.18: 15249 3.18 - 3.75: 27244 3.75 - 4.33: 40035 4.33 - 4.90: 63007 Nonbonded interactions: 145776 Sorted by model distance: nonbonded pdb=" O ASP B 796 " pdb=" O2' C D 26 " model vdw 2.036 2.440 nonbonded pdb=" O PHE A 122 " pdb=" OG SER A 126 " model vdw 2.100 2.440 nonbonded pdb=" OD2 ASP B 681 " pdb=" OG SER B 684 " model vdw 2.115 2.440 nonbonded pdb=" O GLU B1455 " pdb=" O2' C C 42 " model vdw 2.131 2.440 nonbonded pdb=" NH1 ARG B 299 " pdb=" OE2 GLU B 355 " model vdw 2.160 2.520 ... (remaining 145771 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.970 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 54.000 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.010 0.079 17652 Z= 0.670 Angle : 0.856 11.293 24085 Z= 0.475 Chirality : 0.053 0.303 2620 Planarity : 0.005 0.043 2884 Dihedral : 18.989 176.590 7051 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.01 % Favored : 92.78 % Rotamer: Outliers : 5.96 % Allowed : 16.83 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.16), residues: 1953 helix: -1.38 (0.16), residues: 717 sheet: -1.04 (0.29), residues: 253 loop : -2.06 (0.17), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 662 HIS 0.007 0.002 HIS B 784 PHE 0.023 0.003 PHE A 594 TYR 0.021 0.003 TYR A 704 ARG 0.008 0.001 ARG B 596 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 326 time to evaluate : 2.020 Fit side-chains REVERT: A 715 PRO cc_start: 0.7130 (Cg_endo) cc_final: 0.6804 (Cg_exo) REVERT: B 68 GLU cc_start: 0.7582 (tt0) cc_final: 0.7258 (mt-10) REVERT: B 93 LYS cc_start: 0.8210 (mmmt) cc_final: 0.7190 (mptp) REVERT: B 118 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7518 (mtpp) REVERT: B 162 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8533 (tp) REVERT: B 235 ILE cc_start: 0.8010 (pt) cc_final: 0.7703 (pt) REVERT: B 416 ARG cc_start: 0.8154 (mtp85) cc_final: 0.7931 (mtp180) REVERT: B 639 ASP cc_start: 0.7709 (m-30) cc_final: 0.7384 (t70) REVERT: B 1456 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8236 (p) REVERT: B 1618 ASP cc_start: 0.7793 (t0) cc_final: 0.7265 (t0) REVERT: B 1637 ASP cc_start: 0.7386 (t70) cc_final: 0.6892 (t0) outliers start: 103 outliers final: 37 residues processed: 410 average time/residue: 1.2787 time to fit residues: 583.7241 Evaluate side-chains 219 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 675 SER Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1004 THR Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1456 SER Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1514 SER Chi-restraints excluded: chain B residue 1535 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 156 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 133 ASN A 183 HIS A 342 ASN A 476 ASN ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN A 553 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN B 147 HIS B 155 HIS B 345 ASN B 360 ASN B 577 ASN B 614 ASN B 896 ASN ** B 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 973 GLN B 988 ASN B1005 HIS ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1571 ASN ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1684 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17652 Z= 0.191 Angle : 0.593 10.655 24085 Z= 0.312 Chirality : 0.042 0.294 2620 Planarity : 0.004 0.045 2884 Dihedral : 16.707 175.308 3096 Min Nonbonded Distance : 1.521 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 3.47 % Allowed : 22.27 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 1953 helix: 0.71 (0.19), residues: 714 sheet: -0.40 (0.30), residues: 245 loop : -1.21 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 662 HIS 0.009 0.001 HIS B 742 PHE 0.016 0.001 PHE B 453 TYR 0.018 0.001 TYR B1656 ARG 0.009 0.001 ARG B 733 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 202 time to evaluate : 1.916 Fit side-chains REVERT: A 518 TYR cc_start: 0.6826 (m-80) cc_final: 0.6473 (t80) REVERT: B 68 GLU cc_start: 0.7483 (tt0) cc_final: 0.7217 (mt-10) REVERT: B 235 ILE cc_start: 0.8210 (pt) cc_final: 0.7855 (pt) REVERT: B 416 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7936 (mmm160) REVERT: B 499 LYS cc_start: 0.8051 (mmtm) cc_final: 0.7830 (mtmt) REVERT: B 639 ASP cc_start: 0.7788 (m-30) cc_final: 0.7584 (m-30) REVERT: B 745 CYS cc_start: 0.4886 (p) cc_final: 0.4657 (p) REVERT: B 1597 SER cc_start: 0.8677 (t) cc_final: 0.8398 (t) REVERT: B 1618 ASP cc_start: 0.7671 (t0) cc_final: 0.7125 (t70) REVERT: B 1639 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7452 (pmm-80) outliers start: 60 outliers final: 24 residues processed: 248 average time/residue: 1.2776 time to fit residues: 354.9026 Evaluate side-chains 191 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1406 ASP Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1639 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 181 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 183 HIS A 476 ASN ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS A 642 HIS B 34 GLN B 155 HIS B 450 HIS B 950 ASN ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1630 ASN B1666 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17652 Z= 0.413 Angle : 0.684 11.852 24085 Z= 0.356 Chirality : 0.047 0.299 2620 Planarity : 0.005 0.047 2884 Dihedral : 16.492 177.349 3060 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.67 % Rotamer: Outliers : 4.22 % Allowed : 23.08 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.18), residues: 1953 helix: 0.90 (0.19), residues: 723 sheet: -0.17 (0.31), residues: 249 loop : -1.04 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 607 HIS 0.007 0.001 HIS B 155 PHE 0.020 0.002 PHE B 187 TYR 0.025 0.002 TYR A 704 ARG 0.005 0.001 ARG B 596 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 182 time to evaluate : 1.876 Fit side-chains revert: symmetry clash REVERT: B 235 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8200 (pp) REVERT: B 368 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7177 (mm-30) REVERT: B 572 ARG cc_start: 0.8068 (mmt180) cc_final: 0.7852 (mpt90) REVERT: B 625 LYS cc_start: 0.8498 (mtmm) cc_final: 0.8053 (mttp) REVERT: B 639 ASP cc_start: 0.8204 (m-30) cc_final: 0.7678 (t0) REVERT: B 748 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7263 (t0) REVERT: B 837 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8498 (tt) REVERT: B 981 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7765 (p0) REVERT: B 1502 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8157 (t) REVERT: B 1569 SER cc_start: 0.6518 (OUTLIER) cc_final: 0.6045 (p) REVERT: B 1612 HIS cc_start: 0.8339 (p-80) cc_final: 0.7700 (p-80) REVERT: B 1618 ASP cc_start: 0.7882 (t0) cc_final: 0.7257 (t70) REVERT: B 1670 LYS cc_start: 0.8399 (mttp) cc_final: 0.7822 (mppt) outliers start: 73 outliers final: 30 residues processed: 235 average time/residue: 1.3380 time to fit residues: 350.9811 Evaluate side-chains 189 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 152 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 576 ASN Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 748 ASP Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1406 ASP Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1538 LYS Chi-restraints excluded: chain B residue 1539 ASN Chi-restraints excluded: chain B residue 1569 SER Chi-restraints excluded: chain B residue 1629 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 173 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 476 ASN A 541 ASN ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN A 592 ASN B 155 HIS ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1666 ASN B1684 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17652 Z= 0.175 Angle : 0.549 11.420 24085 Z= 0.288 Chirality : 0.041 0.280 2620 Planarity : 0.004 0.050 2884 Dihedral : 16.263 175.074 3052 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.35 % Favored : 95.60 % Rotamer: Outliers : 3.07 % Allowed : 24.58 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 1953 helix: 1.36 (0.20), residues: 723 sheet: 0.16 (0.32), residues: 249 loop : -0.91 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 675 HIS 0.005 0.001 HIS B 903 PHE 0.022 0.001 PHE B 453 TYR 0.019 0.001 TYR A 607 ARG 0.004 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 179 time to evaluate : 1.832 Fit side-chains revert: symmetry clash REVERT: A 231 ARG cc_start: 0.7640 (ptm160) cc_final: 0.7276 (ptp90) REVERT: A 331 MET cc_start: 0.5496 (tpt) cc_final: 0.4339 (mmt) REVERT: A 597 MET cc_start: 0.2851 (mpt) cc_final: 0.2015 (ptp) REVERT: B 184 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7726 (pmtt) REVERT: B 235 ILE cc_start: 0.8545 (pt) cc_final: 0.8187 (pp) REVERT: B 340 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6116 (tt0) REVERT: B 460 GLU cc_start: 0.8201 (tp30) cc_final: 0.7870 (mm-30) REVERT: B 504 MET cc_start: 0.8945 (mmm) cc_final: 0.8654 (mmm) REVERT: B 625 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8059 (mttm) REVERT: B 639 ASP cc_start: 0.8133 (m-30) cc_final: 0.7588 (t70) REVERT: B 649 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: B 650 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7312 (mtm-85) REVERT: B 740 GLU cc_start: 0.7243 (tp30) cc_final: 0.6995 (tp30) REVERT: B 743 GLU cc_start: 0.5563 (OUTLIER) cc_final: 0.4728 (tm-30) REVERT: B 981 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7648 (p0) REVERT: B 1396 LYS cc_start: 0.8090 (tppt) cc_final: 0.7638 (ttpp) REVERT: B 1406 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: B 1502 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8208 (t) REVERT: B 1612 HIS cc_start: 0.8340 (p-80) cc_final: 0.7872 (p-80) REVERT: B 1618 ASP cc_start: 0.7704 (t0) cc_final: 0.7094 (t70) REVERT: B 1670 LYS cc_start: 0.8449 (mttp) cc_final: 0.7914 (mppt) outliers start: 53 outliers final: 19 residues processed: 218 average time/residue: 1.3046 time to fit residues: 318.8604 Evaluate side-chains 182 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 650 ARG Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 981 ASN Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1406 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 173 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN ** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17652 Z= 0.353 Angle : 0.616 10.005 24085 Z= 0.322 Chirality : 0.045 0.301 2620 Planarity : 0.005 0.055 2884 Dihedral : 16.236 176.667 3052 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.16 % Allowed : 23.25 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 1953 helix: 1.22 (0.19), residues: 730 sheet: 0.19 (0.32), residues: 250 loop : -0.95 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 675 HIS 0.006 0.001 HIS B 155 PHE 0.017 0.002 PHE B 187 TYR 0.023 0.002 TYR A 704 ARG 0.008 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 178 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 MET cc_start: 0.5250 (tpt) cc_final: 0.4697 (tpt) REVERT: A 597 MET cc_start: 0.3150 (mpt) cc_final: 0.2848 (ptp) REVERT: B 29 SER cc_start: 0.8152 (OUTLIER) cc_final: 0.7943 (m) REVERT: B 118 LYS cc_start: 0.7778 (mtpt) cc_final: 0.7058 (tppt) REVERT: B 127 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8197 (mp) REVERT: B 173 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8774 (mp) REVERT: B 184 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7814 (pmtt) REVERT: B 235 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8235 (pp) REVERT: B 340 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6470 (tt0) REVERT: B 368 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: B 504 MET cc_start: 0.8946 (mmm) cc_final: 0.8723 (mmm) REVERT: B 572 ARG cc_start: 0.8060 (mmt180) cc_final: 0.7853 (mpt90) REVERT: B 625 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8070 (mttm) REVERT: B 639 ASP cc_start: 0.8173 (m-30) cc_final: 0.7830 (t0) REVERT: B 649 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: B 743 GLU cc_start: 0.5617 (OUTLIER) cc_final: 0.4710 (tm-30) REVERT: B 1396 LYS cc_start: 0.8120 (tppt) cc_final: 0.7730 (ttpp) REVERT: B 1406 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: B 1502 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8320 (t) REVERT: B 1670 LYS cc_start: 0.8538 (mttp) cc_final: 0.7974 (mppt) outliers start: 72 outliers final: 32 residues processed: 228 average time/residue: 1.3184 time to fit residues: 334.8800 Evaluate side-chains 204 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 161 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 904 GLN Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1406 ASP Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1504 THR Chi-restraints excluded: chain B residue 1539 ASN Chi-restraints excluded: chain B residue 1629 LEU Chi-restraints excluded: chain B residue 1639 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.2980 chunk 174 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 193 optimal weight: 8.9990 chunk 160 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A 480 ASN A 642 HIS B 155 HIS ** B 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17652 Z= 0.152 Angle : 0.527 10.310 24085 Z= 0.276 Chirality : 0.040 0.277 2620 Planarity : 0.004 0.049 2884 Dihedral : 16.056 175.417 3050 Min Nonbonded Distance : 1.591 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.95 % Allowed : 24.87 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 1953 helix: 1.54 (0.20), residues: 726 sheet: 0.57 (0.32), residues: 239 loop : -0.82 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 675 HIS 0.004 0.001 HIS B1616 PHE 0.014 0.001 PHE B 800 TYR 0.016 0.001 TYR A 607 ARG 0.006 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 184 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7321 (tt0) REVERT: A 166 ASP cc_start: 0.6716 (m-30) cc_final: 0.6409 (m-30) REVERT: A 216 MET cc_start: 0.7398 (tpt) cc_final: 0.7151 (tpt) REVERT: A 331 MET cc_start: 0.5329 (tpt) cc_final: 0.5110 (mmt) REVERT: A 683 LYS cc_start: 0.7626 (mmtt) cc_final: 0.7402 (mmtt) REVERT: B 118 LYS cc_start: 0.7880 (mtpt) cc_final: 0.7092 (tppt) REVERT: B 184 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7741 (pmtt) REVERT: B 235 ILE cc_start: 0.8570 (pt) cc_final: 0.8233 (pp) REVERT: B 368 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7308 (mm-30) REVERT: B 612 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7507 (mtpp) REVERT: B 625 LYS cc_start: 0.8364 (mtmm) cc_final: 0.7969 (mttm) REVERT: B 639 ASP cc_start: 0.8054 (m-30) cc_final: 0.7581 (t70) REVERT: B 649 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: B 743 GLU cc_start: 0.5689 (OUTLIER) cc_final: 0.4671 (tm-30) REVERT: B 1396 LYS cc_start: 0.8096 (tppt) cc_final: 0.7700 (ttpp) REVERT: B 1502 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8400 (t) REVERT: B 1619 LYS cc_start: 0.7610 (mtpp) cc_final: 0.7392 (mttp) REVERT: B 1670 LYS cc_start: 0.8502 (mttp) cc_final: 0.7953 (mppt) outliers start: 51 outliers final: 24 residues processed: 222 average time/residue: 1.3495 time to fit residues: 332.8525 Evaluate side-chains 192 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 742 HIS Chi-restraints excluded: chain B residue 743 GLU Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1567 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 3.9990 chunk 21 optimal weight: 0.0670 chunk 110 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 120 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 476 ASN A 585 HIS B 155 HIS ** B 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1591 GLN ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17652 Z= 0.185 Angle : 0.536 9.358 24085 Z= 0.280 Chirality : 0.041 0.287 2620 Planarity : 0.004 0.061 2884 Dihedral : 15.990 176.047 3048 Min Nonbonded Distance : 1.595 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.95 % Allowed : 25.27 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 1953 helix: 1.60 (0.20), residues: 724 sheet: 0.63 (0.32), residues: 244 loop : -0.77 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 675 HIS 0.004 0.001 HIS B 155 PHE 0.017 0.001 PHE A 254 TYR 0.017 0.001 TYR A 607 ARG 0.010 0.000 ARG B 733 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 173 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 MET cc_start: 0.7000 (ttt) cc_final: 0.6713 (ttm) REVERT: A 683 LYS cc_start: 0.7646 (mmtt) cc_final: 0.7436 (mmtm) REVERT: B 118 LYS cc_start: 0.7825 (mtpt) cc_final: 0.7095 (tppt) REVERT: B 127 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8087 (mp) REVERT: B 184 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7762 (pmtt) REVERT: B 235 ILE cc_start: 0.8595 (pt) cc_final: 0.8258 (pp) REVERT: B 368 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: B 625 LYS cc_start: 0.8383 (mtmm) cc_final: 0.7900 (mttm) REVERT: B 639 ASP cc_start: 0.8083 (m-30) cc_final: 0.7634 (t70) REVERT: B 649 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: B 1396 LYS cc_start: 0.8099 (tppt) cc_final: 0.7710 (ttpp) REVERT: B 1502 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8427 (t) REVERT: B 1619 LYS cc_start: 0.7685 (mtpp) cc_final: 0.7470 (mttp) REVERT: B 1670 LYS cc_start: 0.8488 (mttp) cc_final: 0.7948 (mppt) outliers start: 51 outliers final: 23 residues processed: 210 average time/residue: 1.4524 time to fit residues: 339.2085 Evaluate side-chains 188 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1406 ASP Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 2.9990 chunk 76 optimal weight: 0.0060 chunk 115 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 476 ASN A 575 ASN B 155 HIS ** B 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17652 Z= 0.236 Angle : 0.552 9.193 24085 Z= 0.288 Chirality : 0.042 0.289 2620 Planarity : 0.004 0.045 2884 Dihedral : 15.980 176.216 3048 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.89 % Allowed : 25.56 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1953 helix: 1.54 (0.19), residues: 723 sheet: 0.47 (0.32), residues: 255 loop : -0.76 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 675 HIS 0.004 0.001 HIS B 155 PHE 0.024 0.002 PHE B 453 TYR 0.017 0.001 TYR A 704 ARG 0.007 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 170 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 590 MET cc_start: 0.7033 (ttt) cc_final: 0.6671 (ttm) REVERT: A 683 LYS cc_start: 0.7673 (mmtt) cc_final: 0.7454 (mmtm) REVERT: A 697 LYS cc_start: 0.7252 (pmtt) cc_final: 0.6859 (tppt) REVERT: B 118 LYS cc_start: 0.7772 (mtpt) cc_final: 0.7047 (tptt) REVERT: B 127 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8110 (mp) REVERT: B 184 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7785 (pmtt) REVERT: B 235 ILE cc_start: 0.8627 (pt) cc_final: 0.8254 (pp) REVERT: B 368 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7339 (mm-30) REVERT: B 625 LYS cc_start: 0.8401 (mtmm) cc_final: 0.7965 (mttm) REVERT: B 639 ASP cc_start: 0.8097 (m-30) cc_final: 0.7792 (t0) REVERT: B 649 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: B 1396 LYS cc_start: 0.8115 (tppt) cc_final: 0.7757 (ttpp) REVERT: B 1502 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8461 (t) REVERT: B 1619 LYS cc_start: 0.7671 (mtpp) cc_final: 0.7461 (mttp) REVERT: B 1670 LYS cc_start: 0.8533 (mttp) cc_final: 0.7982 (mppt) outliers start: 50 outliers final: 33 residues processed: 204 average time/residue: 1.4391 time to fit residues: 324.4905 Evaluate side-chains 199 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 161 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 597 MET Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 698 LYS Chi-restraints excluded: chain B residue 706 ASN Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1406 ASP Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1504 THR Chi-restraints excluded: chain B residue 1539 ASN Chi-restraints excluded: chain B residue 1629 LEU Chi-restraints excluded: chain B residue 1639 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 108 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 189 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 363 ASN A 476 ASN A 575 ASN B 155 HIS B 577 ASN ** B 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 17652 Z= 0.155 Angle : 0.523 9.221 24085 Z= 0.273 Chirality : 0.040 0.278 2620 Planarity : 0.004 0.045 2884 Dihedral : 15.873 175.598 3048 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.43 % Allowed : 26.55 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.19), residues: 1953 helix: 1.67 (0.20), residues: 725 sheet: 0.71 (0.33), residues: 238 loop : -0.71 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 675 HIS 0.004 0.001 HIS B1616 PHE 0.021 0.001 PHE A 254 TYR 0.015 0.001 TYR A 607 ARG 0.009 0.000 ARG B 733 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 177 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.6835 (m-30) cc_final: 0.6510 (m-30) REVERT: A 590 MET cc_start: 0.7072 (ttt) cc_final: 0.6794 (ttm) REVERT: B 127 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8099 (mp) REVERT: B 184 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7722 (pmtt) REVERT: B 235 ILE cc_start: 0.8590 (pt) cc_final: 0.8248 (pp) REVERT: B 368 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7314 (mm-30) REVERT: B 404 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6819 (tp30) REVERT: B 625 LYS cc_start: 0.8357 (mtmm) cc_final: 0.7905 (mttm) REVERT: B 639 ASP cc_start: 0.8070 (m-30) cc_final: 0.7759 (t0) REVERT: B 649 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: B 1396 LYS cc_start: 0.8082 (tppt) cc_final: 0.7706 (ttpp) REVERT: B 1619 LYS cc_start: 0.7662 (mtpp) cc_final: 0.7448 (mttp) REVERT: B 1670 LYS cc_start: 0.8530 (mttp) cc_final: 0.7904 (mppt) outliers start: 42 outliers final: 23 residues processed: 203 average time/residue: 1.3501 time to fit residues: 305.0384 Evaluate side-chains 189 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1406 ASP Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1504 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 132 optimal weight: 0.9980 chunk 199 optimal weight: 8.9990 chunk 183 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 476 ASN A 575 ASN B 155 HIS B 577 ASN ** B 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17652 Z= 0.181 Angle : 0.534 9.241 24085 Z= 0.278 Chirality : 0.040 0.284 2620 Planarity : 0.004 0.044 2884 Dihedral : 15.823 176.144 3047 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.31 % Allowed : 27.07 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 1953 helix: 1.70 (0.19), residues: 723 sheet: 0.63 (0.32), residues: 250 loop : -0.67 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 675 HIS 0.004 0.001 HIS B 155 PHE 0.029 0.001 PHE A 254 TYR 0.016 0.001 TYR A 607 ARG 0.009 0.000 ARG B 733 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 167 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.6857 (m-30) cc_final: 0.6519 (m-30) REVERT: A 225 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: A 590 MET cc_start: 0.7065 (ttt) cc_final: 0.6681 (ttm) REVERT: A 697 LYS cc_start: 0.7533 (pmtt) cc_final: 0.6987 (tppt) REVERT: B 118 LYS cc_start: 0.7721 (mtpt) cc_final: 0.7043 (tptt) REVERT: B 127 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8095 (mp) REVERT: B 184 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7733 (pmtt) REVERT: B 235 ILE cc_start: 0.8606 (pt) cc_final: 0.8266 (pp) REVERT: B 277 GLU cc_start: 0.7243 (pp20) cc_final: 0.7039 (pp20) REVERT: B 368 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7305 (mm-30) REVERT: B 404 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6882 (tp30) REVERT: B 625 LYS cc_start: 0.8365 (mtmm) cc_final: 0.7907 (mttm) REVERT: B 639 ASP cc_start: 0.8086 (m-30) cc_final: 0.7664 (t0) REVERT: B 649 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: B 1396 LYS cc_start: 0.8057 (tppt) cc_final: 0.7707 (ttpp) REVERT: B 1619 LYS cc_start: 0.7691 (mtpp) cc_final: 0.7469 (mttp) REVERT: B 1670 LYS cc_start: 0.8550 (mttp) cc_final: 0.7928 (mppt) outliers start: 40 outliers final: 25 residues processed: 198 average time/residue: 1.3756 time to fit residues: 304.3075 Evaluate side-chains 191 residues out of total 1729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 225 TYR Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 491 PHE Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 270 LYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 825 PHE Chi-restraints excluded: chain B residue 861 ILE Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1406 ASP Chi-restraints excluded: chain B residue 1419 ASP Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1496 VAL Chi-restraints excluded: chain B residue 1504 THR Chi-restraints excluded: chain B residue 1629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 6.9990 chunk 146 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 476 ASN A 575 ASN B 155 HIS B 429 GLN B 577 ASN ** B 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.157726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.101180 restraints weight = 19273.929| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.45 r_work: 0.3030 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 17652 Z= 0.162 Angle : 0.524 9.252 24085 Z= 0.273 Chirality : 0.040 0.279 2620 Planarity : 0.004 0.045 2884 Dihedral : 15.754 175.825 3045 Min Nonbonded Distance : 1.632 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.08 % Allowed : 27.47 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 1953 helix: 1.72 (0.20), residues: 726 sheet: 0.68 (0.32), residues: 245 loop : -0.66 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 675 HIS 0.004 0.001 HIS B1616 PHE 0.014 0.001 PHE B 800 TYR 0.015 0.001 TYR A 607 ARG 0.008 0.000 ARG B 733 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6446.74 seconds wall clock time: 114 minutes 56.73 seconds (6896.73 seconds total)