Starting phenix.real_space_refine on Thu Mar 14 14:08:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcv_20308/03_2024/6pcv_20308.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcv_20308/03_2024/6pcv_20308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcv_20308/03_2024/6pcv_20308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcv_20308/03_2024/6pcv_20308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcv_20308/03_2024/6pcv_20308.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcv_20308/03_2024/6pcv_20308.pdb" } resolution = 3.2 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= 0.009 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: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5666 2.51 5 N 1596 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 516": "NH1" <-> "NH2" Residue "A TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 520": "NH1" <-> "NH2" Residue "A ASP 550": "OD1" <-> "OD2" Residue "A ARG 561": "NH1" <-> "NH2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 582": "OE1" <-> "OE2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A ASP 638": "OD1" <-> "OD2" Residue "A ARG 653": "NH1" <-> "NH2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "A PHE 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A ARG 777": "NH1" <-> "NH2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "A TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 797": "OE1" <-> "OE2" Residue "A ARG 799": "NH1" <-> "NH2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A ASP 847": "OD1" <-> "OD2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A PHE 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 978": "OE1" <-> "OE2" Residue "A GLU 1355": "OE1" <-> "OE2" Residue "A GLU 1357": "OE1" <-> "OE2" Residue "A ASP 1362": "OD1" <-> "OD2" Residue "A GLU 1369": "OE1" <-> "OE2" Residue "A GLU 1391": "OE1" <-> "OE2" Residue "A ASP 1407": "OD1" <-> "OD2" Residue "A ASP 1417": "OD1" <-> "OD2" Residue "A PHE 1468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1476": "OE1" <-> "OE2" Residue "A ASP 1488": "OD1" <-> "OD2" Residue "A ASP 1492": "OD1" <-> "OD2" Residue "A TYR 1504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1540": "OD1" <-> "OD2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 63": "OE1" <-> "OE2" Residue "G PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9035 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5946 Classifications: {'peptide': 754} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 718} Chain breaks: 6 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 482 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Time building chain proxies: 5.23, per 1000 atoms: 0.58 Number of scatterers: 9035 At special positions: 0 Unit cell: (81, 105, 108, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 1708 8.00 N 1596 7.00 C 5666 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: 3.43 Conformation dependent library (CDL) restraints added in 1.8 seconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 33.9% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 509 through 522 Processing helix chain 'A' and resid 545 through 556 Processing helix chain 'A' and resid 560 through 574 Processing helix chain 'A' and resid 596 through 603 Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 680 through 694 Processing helix chain 'A' and resid 738 through 744 Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 791 through 803 Processing helix chain 'A' and resid 879 through 895 Processing helix chain 'A' and resid 933 through 947 removed outlier: 4.166A pdb=" N ARG A 947 " --> pdb=" O GLN A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 968 removed outlier: 3.622A pdb=" N PHE A 967 " --> pdb=" O GLY A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1347 removed outlier: 3.985A pdb=" N ALA A1333 " --> pdb=" O GLN A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1375 Processing helix chain 'A' and resid 1389 through 1407 Processing helix chain 'A' and resid 1444 through 1450 Processing helix chain 'A' and resid 1454 through 1458 removed outlier: 3.598A pdb=" N GLY A1457 " --> pdb=" O ARG A1454 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1518 removed outlier: 4.311A pdb=" N ALA A1486 " --> pdb=" O GLY A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1551 removed outlier: 5.080A pdb=" N ARG A1534 " --> pdb=" O ASP A1530 " (cutoff:3.500A) Proline residue: A1535 - end of helix removed outlier: 3.934A pdb=" N ALA A1538 " --> pdb=" O ARG A1534 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1575 removed outlier: 3.627A pdb=" N ILE A1567 " --> pdb=" O GLY A1563 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A1569 " --> pdb=" O ILE A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1587 through 1605 Processing helix chain 'A' and resid 1612 through 1623 removed outlier: 3.913A pdb=" N ARG A1621 " --> pdb=" O THR A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1634 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 25 Processing helix chain 'G' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 532 through 534 Processing sheet with id=AA2, first strand: chain 'A' and resid 542 through 544 Processing sheet with id=AA3, first strand: chain 'A' and resid 668 through 671 removed outlier: 6.446A pdb=" N LEU A 701 " --> pdb=" O TYR A 669 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE A 671 " --> pdb=" O ARG A 699 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG A 699 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 702 " --> pdb=" O LYS A 624 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU A 617 " --> pdb=" O GLU A 858 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU A 858 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG A 866 " --> pdb=" O PRO A 982 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 981 " --> pdb=" O SER A1016 " (cutoff:3.500A) removed outlier: 16.226A pdb=" N ALA A1577 " --> pdb=" O TYR A1017 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N GLN A1019 " --> pdb=" O ALA A1577 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N GLN A1579 " --> pdb=" O GLN A1019 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS A1021 " --> pdb=" O GLN A1579 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL A1581 " --> pdb=" O CYS A1021 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N THR A1023 " --> pdb=" O VAL A1581 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N CYS A1583 " --> pdb=" O THR A1023 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET A1025 " --> pdb=" O CYS A1583 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A1377 " --> pdb=" O CYS A1578 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N MET A1580 " --> pdb=" O LEU A1377 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N HIS A1379 " --> pdb=" O MET A1580 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N MET A1582 " --> pdb=" O HIS A1379 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLN A1381 " --> pdb=" O MET A1582 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL A1409 " --> pdb=" O LEU A1463 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N THR A1410 " --> pdb=" O VAL A1439 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N PHE A1441 " --> pdb=" O THR A1410 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER A1412 " --> pdb=" O PHE A1441 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU A1443 " --> pdb=" O SER A1412 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS A1414 " --> pdb=" O LEU A1443 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 637 through 640 removed outlier: 6.731A pdb=" N ASP A 638 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 707 through 713 removed outlier: 7.325A pdb=" N THR A 843 " --> pdb=" O VAL A 754 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL A 754 " --> pdb=" O THR A 843 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR A 845 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 721 through 725 removed outlier: 6.377A pdb=" N GLN A 722 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.751A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.675A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.246A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.251A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.659A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.607A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.141A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3005 1.34 - 1.46: 1648 1.46 - 1.58: 4458 1.58 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 9202 Sorted by residual: bond pdb=" CB VAL A 856 " pdb=" CG2 VAL A 856 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.16e+00 bond pdb=" C SER A 949 " pdb=" N PRO A 950 " ideal model delta sigma weight residual 1.329 1.349 -0.020 1.18e-02 7.18e+03 2.94e+00 bond pdb=" CG LEU A1383 " pdb=" CD1 LEU A1383 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.41e+00 bond pdb=" C PRO A 950 " pdb=" N PRO A 951 " ideal model delta sigma weight residual 1.338 1.365 -0.027 1.90e-02 2.77e+03 2.05e+00 bond pdb=" C ALA A 764 " pdb=" N PRO A 765 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.23e-02 6.61e+03 1.96e+00 ... (remaining 9197 not shown) Histogram of bond angle deviations from ideal: 98.59 - 107.48: 363 107.48 - 116.36: 5821 116.36 - 125.24: 6105 125.24 - 134.13: 155 134.13 - 143.01: 1 Bond angle restraints: 12445 Sorted by residual: angle pdb=" C PRO A 950 " pdb=" N PRO A 951 " pdb=" CA PRO A 951 " ideal model delta sigma weight residual 127.00 143.01 -16.01 2.40e+00 1.74e-01 4.45e+01 angle pdb=" C LEU A1564 " pdb=" N ILE A1565 " pdb=" CA ILE A1565 " ideal model delta sigma weight residual 120.24 124.20 -3.96 6.30e-01 2.52e+00 3.95e+01 angle pdb=" C PRO A 950 " pdb=" N PRO A 951 " pdb=" CD PRO A 951 " ideal model delta sigma weight residual 120.60 107.89 12.71 2.20e+00 2.07e-01 3.34e+01 angle pdb=" N PRO A 950 " pdb=" CA PRO A 950 " pdb=" C PRO A 950 " ideal model delta sigma weight residual 110.70 115.12 -4.42 1.22e+00 6.72e-01 1.31e+01 angle pdb=" N SER A 949 " pdb=" CA SER A 949 " pdb=" C SER A 949 " ideal model delta sigma weight residual 109.81 117.53 -7.72 2.21e+00 2.05e-01 1.22e+01 ... (remaining 12440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 5045 17.84 - 35.69: 438 35.69 - 53.53: 78 53.53 - 71.38: 17 71.38 - 89.22: 8 Dihedral angle restraints: 5586 sinusoidal: 2233 harmonic: 3353 Sorted by residual: dihedral pdb=" CA TYR A1420 " pdb=" C TYR A1420 " pdb=" N VAL A1421 " pdb=" CA VAL A1421 " ideal model delta harmonic sigma weight residual 180.00 156.79 23.21 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA VAL A1421 " pdb=" C VAL A1421 " pdb=" N ALA A1422 " pdb=" CA ALA A1422 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ARG A1626 " pdb=" C ARG A1626 " pdb=" N VAL A1627 " pdb=" CA VAL A1627 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 5583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 918 0.050 - 0.100: 345 0.100 - 0.150: 99 0.150 - 0.200: 24 0.200 - 0.250: 6 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CB ILE A 529 " pdb=" CA ILE A 529 " pdb=" CG1 ILE A 529 " pdb=" CG2 ILE A 529 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE A 873 " pdb=" CA ILE A 873 " pdb=" CG1 ILE A 873 " pdb=" CG2 ILE A 873 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1389 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 712 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO A 713 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 713 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 713 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1480 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A1481 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A1481 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1481 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.042 5.00e-02 4.00e+02 6.30e-02 6.34e+00 pdb=" N PRO B 236 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.035 5.00e-02 4.00e+02 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1680 2.77 - 3.30: 8280 3.30 - 3.83: 15757 3.83 - 4.37: 18379 4.37 - 4.90: 31956 Nonbonded interactions: 76052 Sorted by model distance: nonbonded pdb=" OG SER A1359 " pdb=" OD1 ASP A1362 " model vdw 2.235 2.440 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.289 2.440 nonbonded pdb=" O ASP A1398 " pdb=" OG1 THR A1402 " model vdw 2.289 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.302 2.440 ... (remaining 76047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.910 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.740 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 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 : 0.006 0.061 9202 Z= 0.386 Angle : 0.978 16.008 12445 Z= 0.530 Chirality : 0.059 0.250 1392 Planarity : 0.007 0.065 1621 Dihedral : 14.309 89.224 3416 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.71 % Allowed : 8.97 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.20), residues: 1137 helix: -2.19 (0.19), residues: 383 sheet: -2.10 (0.28), residues: 249 loop : -2.20 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A1367 HIS 0.010 0.002 HIS A1379 PHE 0.020 0.002 PHE B 253 TYR 0.012 0.002 TYR A 859 ARG 0.013 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 335 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 LYS cc_start: 0.8435 (pttt) cc_final: 0.8053 (ptpp) REVERT: A 531 ASP cc_start: 0.7104 (p0) cc_final: 0.6448 (p0) REVERT: A 547 LYS cc_start: 0.7394 (tptm) cc_final: 0.6827 (tppt) REVERT: A 563 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7053 (mt-10) REVERT: A 565 VAL cc_start: 0.8498 (m) cc_final: 0.8281 (p) REVERT: A 574 ASN cc_start: 0.7512 (m110) cc_final: 0.7108 (m110) REVERT: A 577 MET cc_start: 0.7258 (ptp) cc_final: 0.6969 (ptt) REVERT: A 580 VAL cc_start: 0.8366 (m) cc_final: 0.8146 (t) REVERT: A 619 GLU cc_start: 0.7001 (tt0) cc_final: 0.6760 (tt0) REVERT: A 639 ILE cc_start: 0.8629 (pt) cc_final: 0.8325 (pt) REVERT: A 644 LYS cc_start: 0.8835 (mptt) cc_final: 0.8605 (mmtm) REVERT: A 696 ARG cc_start: 0.7382 (mtt-85) cc_final: 0.7109 (mtt-85) REVERT: A 709 ILE cc_start: 0.8468 (pt) cc_final: 0.8051 (pt) REVERT: A 723 ILE cc_start: 0.8377 (mt) cc_final: 0.8097 (mm) REVERT: A 754 VAL cc_start: 0.8084 (t) cc_final: 0.7834 (p) REVERT: A 759 VAL cc_start: 0.9192 (m) cc_final: 0.8618 (p) REVERT: A 777 ARG cc_start: 0.7635 (ptp-170) cc_final: 0.7403 (ptp-170) REVERT: A 858 GLU cc_start: 0.7048 (pp20) cc_final: 0.6663 (pt0) REVERT: A 872 LYS cc_start: 0.7800 (mtmm) cc_final: 0.7516 (mtpp) REVERT: A 882 LEU cc_start: 0.8091 (tp) cc_final: 0.7858 (tp) REVERT: A 1019 GLN cc_start: 0.7469 (tt0) cc_final: 0.7008 (tm-30) REVERT: A 1320 GLN cc_start: 0.6942 (mm-40) cc_final: 0.6422 (mm-40) REVERT: A 1322 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7677 (ptm-80) REVERT: A 1353 ASN cc_start: 0.7315 (m-40) cc_final: 0.6903 (m-40) REVERT: A 1366 LYS cc_start: 0.8362 (pttp) cc_final: 0.8074 (pttp) REVERT: A 1405 GLU cc_start: 0.6598 (tp30) cc_final: 0.6197 (tp30) REVERT: A 1443 LEU cc_start: 0.8578 (mp) cc_final: 0.8349 (mm) REVERT: A 1450 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7802 (mtpp) REVERT: A 1507 LYS cc_start: 0.8233 (mttt) cc_final: 0.7822 (mttp) REVERT: A 1580 MET cc_start: 0.6530 (mtp) cc_final: 0.6263 (mtp) REVERT: A 1614 MET cc_start: 0.7973 (tpt) cc_final: 0.7764 (tpt) REVERT: A 1632 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7680 (mttp) REVERT: A 1648 TYR cc_start: 0.7379 (m-80) cc_final: 0.7156 (m-80) REVERT: B 4 LEU cc_start: 0.8304 (mm) cc_final: 0.8100 (mt) REVERT: B 15 LYS cc_start: 0.8756 (mttp) cc_final: 0.8439 (mttp) REVERT: B 97 SER cc_start: 0.8223 (p) cc_final: 0.7966 (m) REVERT: B 102 THR cc_start: 0.7819 (t) cc_final: 0.7604 (t) REVERT: B 118 ASP cc_start: 0.6668 (t0) cc_final: 0.6395 (t0) REVERT: B 123 ILE cc_start: 0.8038 (mm) cc_final: 0.7791 (mm) REVERT: B 188 MET cc_start: 0.6764 (mmm) cc_final: 0.6559 (mmm) REVERT: B 196 THR cc_start: 0.8193 (p) cc_final: 0.7535 (t) REVERT: B 247 ASP cc_start: 0.7002 (t70) cc_final: 0.6302 (t0) REVERT: B 250 CYS cc_start: 0.6716 (m) cc_final: 0.6247 (m) REVERT: B 251 ARG cc_start: 0.7561 (mtt-85) cc_final: 0.6986 (mmm-85) REVERT: B 279 SER cc_start: 0.8579 (m) cc_final: 0.8348 (t) REVERT: B 289 TYR cc_start: 0.8270 (m-80) cc_final: 0.8068 (m-80) REVERT: B 336 LEU cc_start: 0.7633 (mt) cc_final: 0.7368 (mm) REVERT: B 338 ILE cc_start: 0.8451 (mm) cc_final: 0.8125 (mm) REVERT: G 15 LEU cc_start: 0.8784 (mt) cc_final: 0.8412 (mt) REVERT: G 17 GLU cc_start: 0.8276 (pt0) cc_final: 0.7960 (mt-10) REVERT: G 18 GLN cc_start: 0.8144 (tp40) cc_final: 0.7345 (tp40) REVERT: G 19 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8652 (mp) REVERT: G 20 LYS cc_start: 0.8599 (ptmt) cc_final: 0.8188 (ptpp) REVERT: G 22 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7247 (mt-10) REVERT: G 38 MET cc_start: 0.7271 (ttp) cc_final: 0.6990 (tmm) outliers start: 7 outliers final: 3 residues processed: 339 average time/residue: 0.2912 time to fit residues: 125.3258 Evaluate side-chains 280 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 276 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 HIS A 643 ASN A 749 GLN A 802 GLN A 975 ASN A1019 GLN A1329 GLN A1370 GLN A1415 GLN A1490 GLN A1503 GLN A1588 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 35 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9202 Z= 0.273 Angle : 0.655 8.788 12445 Z= 0.343 Chirality : 0.044 0.142 1392 Planarity : 0.005 0.060 1621 Dihedral : 5.456 41.914 1261 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.08 % Allowed : 15.19 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.23), residues: 1137 helix: -0.06 (0.25), residues: 384 sheet: -1.73 (0.29), residues: 249 loop : -1.74 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 297 HIS 0.005 0.001 HIS A1447 PHE 0.021 0.002 PHE A 637 TYR 0.016 0.001 TYR A 534 ARG 0.007 0.001 ARG A 699 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 284 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 LYS cc_start: 0.8510 (pttt) cc_final: 0.8191 (ptpp) REVERT: A 540 LYS cc_start: 0.7932 (tptt) cc_final: 0.7519 (tptp) REVERT: A 547 LYS cc_start: 0.7678 (tptm) cc_final: 0.7105 (tppt) REVERT: A 563 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7167 (mt-10) REVERT: A 565 VAL cc_start: 0.8499 (m) cc_final: 0.8276 (p) REVERT: A 574 ASN cc_start: 0.7449 (m110) cc_final: 0.6827 (m110) REVERT: A 587 ARG cc_start: 0.7725 (ttp-110) cc_final: 0.7382 (ttp-110) REVERT: A 593 PHE cc_start: 0.6793 (m-10) cc_final: 0.6469 (m-10) REVERT: A 638 ASP cc_start: 0.6830 (p0) cc_final: 0.6613 (p0) REVERT: A 644 LYS cc_start: 0.8889 (mptt) cc_final: 0.8654 (mmtm) REVERT: A 683 GLU cc_start: 0.7190 (tt0) cc_final: 0.6874 (tt0) REVERT: A 696 ARG cc_start: 0.7382 (mtt-85) cc_final: 0.6973 (mtt-85) REVERT: A 701 LEU cc_start: 0.8206 (mt) cc_final: 0.6067 (mt) REVERT: A 705 LYS cc_start: 0.8015 (mtmm) cc_final: 0.7683 (mttm) REVERT: A 723 ILE cc_start: 0.8379 (mt) cc_final: 0.8128 (mm) REVERT: A 754 VAL cc_start: 0.8384 (t) cc_final: 0.8124 (p) REVERT: A 777 ARG cc_start: 0.7654 (ptp-170) cc_final: 0.7397 (ptp90) REVERT: A 796 GLN cc_start: 0.7901 (pt0) cc_final: 0.7395 (pt0) REVERT: A 858 GLU cc_start: 0.7081 (pp20) cc_final: 0.6617 (tm-30) REVERT: A 872 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7318 (mtpp) REVERT: A 939 GLU cc_start: 0.7916 (tp30) cc_final: 0.7624 (tp30) REVERT: A 1019 GLN cc_start: 0.7553 (tt0) cc_final: 0.7137 (tm-30) REVERT: A 1326 ILE cc_start: 0.8276 (pt) cc_final: 0.8033 (tt) REVERT: A 1327 PHE cc_start: 0.7878 (t80) cc_final: 0.7634 (t80) REVERT: A 1340 GLU cc_start: 0.6650 (tp30) cc_final: 0.6297 (tp30) REVERT: A 1343 LEU cc_start: 0.8283 (mp) cc_final: 0.8027 (mm) REVERT: A 1353 ASN cc_start: 0.7480 (m-40) cc_final: 0.7083 (m-40) REVERT: A 1358 GLU cc_start: 0.6724 (tt0) cc_final: 0.6431 (tt0) REVERT: A 1366 LYS cc_start: 0.8492 (pttp) cc_final: 0.8062 (ttpp) REVERT: A 1370 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7721 (tm130) REVERT: A 1405 GLU cc_start: 0.6580 (tp30) cc_final: 0.6013 (tp30) REVERT: A 1431 GLU cc_start: 0.6768 (tm-30) cc_final: 0.6319 (tm-30) REVERT: A 1443 LEU cc_start: 0.8617 (mp) cc_final: 0.8218 (mm) REVERT: A 1450 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7803 (mttp) REVERT: A 1491 GLN cc_start: 0.7624 (tp-100) cc_final: 0.7117 (tm-30) REVERT: A 1507 LYS cc_start: 0.8237 (mttt) cc_final: 0.7837 (mttp) REVERT: A 1580 MET cc_start: 0.6503 (mtp) cc_final: 0.6240 (mtp) REVERT: A 1597 GLU cc_start: 0.6888 (tt0) cc_final: 0.6672 (tt0) REVERT: A 1611 LYS cc_start: 0.7421 (OUTLIER) cc_final: 0.7104 (ttpt) REVERT: A 1614 MET cc_start: 0.7913 (tpt) cc_final: 0.7607 (tpt) REVERT: A 1632 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7646 (mtmm) REVERT: A 1646 ARG cc_start: 0.6974 (tpt-90) cc_final: 0.6693 (ttt-90) REVERT: A 1648 TYR cc_start: 0.7506 (m-80) cc_final: 0.7015 (m-10) REVERT: B 4 LEU cc_start: 0.8205 (mm) cc_final: 0.7998 (mt) REVERT: B 8 ARG cc_start: 0.8337 (mtt90) cc_final: 0.8000 (mtt90) REVERT: B 15 LYS cc_start: 0.8837 (mttp) cc_final: 0.8535 (mttp) REVERT: B 61 MET cc_start: 0.7441 (ppp) cc_final: 0.7028 (ptm) REVERT: B 78 LYS cc_start: 0.8261 (mtpp) cc_final: 0.8023 (mtpp) REVERT: B 79 LEU cc_start: 0.8447 (mt) cc_final: 0.8229 (mt) REVERT: B 118 ASP cc_start: 0.6907 (t0) cc_final: 0.6658 (t0) REVERT: B 146 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8280 (tt) REVERT: B 168 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7880 (tt) REVERT: B 188 MET cc_start: 0.6496 (mmm) cc_final: 0.5721 (mmm) REVERT: B 247 ASP cc_start: 0.7277 (t70) cc_final: 0.6537 (t0) REVERT: B 251 ARG cc_start: 0.7564 (mtt-85) cc_final: 0.6882 (mmt90) REVERT: B 279 SER cc_start: 0.8579 (m) cc_final: 0.8280 (t) REVERT: B 289 TYR cc_start: 0.8286 (m-80) cc_final: 0.8025 (m-80) REVERT: B 336 LEU cc_start: 0.7642 (mt) cc_final: 0.7387 (mm) REVERT: G 15 LEU cc_start: 0.8735 (mt) cc_final: 0.8381 (mt) REVERT: G 18 GLN cc_start: 0.8226 (tp40) cc_final: 0.6295 (tp40) REVERT: G 19 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8676 (mp) REVERT: G 22 GLU cc_start: 0.8061 (mt-10) cc_final: 0.6983 (mt-10) outliers start: 40 outliers final: 10 residues processed: 308 average time/residue: 0.2706 time to fit residues: 106.7783 Evaluate side-chains 285 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 270 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1582 MET Chi-restraints excluded: chain A residue 1611 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 30 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 HIS A 749 GLN ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9202 Z= 0.369 Angle : 0.689 9.264 12445 Z= 0.359 Chirality : 0.046 0.285 1392 Planarity : 0.005 0.060 1621 Dihedral : 5.234 29.777 1259 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.28 % Allowed : 18.65 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.25), residues: 1137 helix: 0.72 (0.27), residues: 382 sheet: -1.60 (0.29), residues: 248 loop : -1.49 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 297 HIS 0.005 0.001 HIS A1447 PHE 0.025 0.002 PHE A 637 TYR 0.018 0.002 TYR B 145 ARG 0.007 0.001 ARG A 775 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 282 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7674 (tt) REVERT: A 511 MET cc_start: 0.6991 (tpp) cc_final: 0.6749 (mmm) REVERT: A 540 LYS cc_start: 0.7867 (tptt) cc_final: 0.7489 (tptp) REVERT: A 547 LYS cc_start: 0.7879 (tptm) cc_final: 0.7150 (tppt) REVERT: A 555 GLN cc_start: 0.7364 (mm-40) cc_final: 0.7143 (mp10) REVERT: A 563 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7227 (mt-10) REVERT: A 565 VAL cc_start: 0.8585 (m) cc_final: 0.8364 (p) REVERT: A 574 ASN cc_start: 0.7536 (m110) cc_final: 0.6894 (m110) REVERT: A 577 MET cc_start: 0.7215 (ptp) cc_final: 0.6582 (mtt) REVERT: A 618 VAL cc_start: 0.8185 (p) cc_final: 0.7959 (t) REVERT: A 638 ASP cc_start: 0.6856 (p0) cc_final: 0.6640 (p0) REVERT: A 644 LYS cc_start: 0.8831 (mptt) cc_final: 0.8569 (mmtm) REVERT: A 683 GLU cc_start: 0.7248 (tt0) cc_final: 0.6888 (tt0) REVERT: A 687 ILE cc_start: 0.8014 (mt) cc_final: 0.7726 (mm) REVERT: A 696 ARG cc_start: 0.7400 (mtt-85) cc_final: 0.7170 (mtt-85) REVERT: A 705 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7613 (mttm) REVERT: A 723 ILE cc_start: 0.8430 (mt) cc_final: 0.8136 (mm) REVERT: A 777 ARG cc_start: 0.7711 (ptp-170) cc_final: 0.7409 (ptp90) REVERT: A 796 GLN cc_start: 0.7942 (pt0) cc_final: 0.7366 (pt0) REVERT: A 852 GLU cc_start: 0.7163 (pt0) cc_final: 0.6758 (pp20) REVERT: A 858 GLU cc_start: 0.7236 (pp20) cc_final: 0.6702 (pt0) REVERT: A 872 LYS cc_start: 0.7821 (mtmm) cc_final: 0.7306 (mtpp) REVERT: A 874 VAL cc_start: 0.8604 (t) cc_final: 0.8317 (m) REVERT: A 882 LEU cc_start: 0.8356 (tp) cc_final: 0.8019 (tp) REVERT: A 939 GLU cc_start: 0.7986 (tp30) cc_final: 0.7752 (tp30) REVERT: A 940 PHE cc_start: 0.8754 (m-10) cc_final: 0.8416 (m-10) REVERT: A 1019 GLN cc_start: 0.7634 (tt0) cc_final: 0.7224 (tt0) REVERT: A 1020 HIS cc_start: 0.7622 (m-70) cc_final: 0.7385 (m-70) REVERT: A 1326 ILE cc_start: 0.8291 (pt) cc_final: 0.8006 (tt) REVERT: A 1327 PHE cc_start: 0.7969 (t80) cc_final: 0.7712 (t80) REVERT: A 1340 GLU cc_start: 0.6739 (tp30) cc_final: 0.6422 (tp30) REVERT: A 1343 LEU cc_start: 0.8266 (mp) cc_final: 0.8021 (mm) REVERT: A 1358 GLU cc_start: 0.6850 (tt0) cc_final: 0.6548 (tt0) REVERT: A 1366 LYS cc_start: 0.8525 (pttp) cc_final: 0.8080 (ttpp) REVERT: A 1405 GLU cc_start: 0.6671 (tp30) cc_final: 0.6062 (tp30) REVERT: A 1412 SER cc_start: 0.8025 (m) cc_final: 0.7750 (p) REVERT: A 1428 TYR cc_start: 0.7841 (m-10) cc_final: 0.7396 (m-10) REVERT: A 1431 GLU cc_start: 0.6787 (tm-30) cc_final: 0.6326 (tm-30) REVERT: A 1443 LEU cc_start: 0.8575 (mp) cc_final: 0.8341 (mm) REVERT: A 1450 LYS cc_start: 0.8314 (mmtp) cc_final: 0.8052 (mmtm) REVERT: A 1469 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8844 (p) REVERT: A 1491 GLN cc_start: 0.7596 (tp-100) cc_final: 0.7152 (tm-30) REVERT: A 1507 LYS cc_start: 0.8276 (mttt) cc_final: 0.7853 (mttp) REVERT: A 1565 ILE cc_start: 0.8446 (mt) cc_final: 0.8080 (mm) REVERT: A 1596 LEU cc_start: 0.7130 (mt) cc_final: 0.6737 (mt) REVERT: A 1611 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7192 (ttpt) REVERT: A 1614 MET cc_start: 0.7882 (tpt) cc_final: 0.7667 (tpt) REVERT: A 1632 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7591 (mtmm) REVERT: B 8 ARG cc_start: 0.8292 (mtt90) cc_final: 0.8015 (mtt90) REVERT: B 15 LYS cc_start: 0.8907 (mttp) cc_final: 0.8613 (mttp) REVERT: B 78 LYS cc_start: 0.8290 (mtpp) cc_final: 0.8063 (mmmt) REVERT: B 79 LEU cc_start: 0.8513 (mt) cc_final: 0.8291 (mt) REVERT: B 118 ASP cc_start: 0.7145 (t0) cc_final: 0.6838 (t0) REVERT: B 168 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7793 (tt) REVERT: B 188 MET cc_start: 0.6524 (mmm) cc_final: 0.6091 (mmm) REVERT: B 247 ASP cc_start: 0.7429 (t70) cc_final: 0.6673 (t0) REVERT: B 251 ARG cc_start: 0.7592 (mtt-85) cc_final: 0.6848 (mmt90) REVERT: B 260 GLU cc_start: 0.6817 (tt0) cc_final: 0.5999 (tt0) REVERT: B 279 SER cc_start: 0.8541 (m) cc_final: 0.8205 (t) REVERT: B 289 TYR cc_start: 0.8330 (m-80) cc_final: 0.8058 (m-80) REVERT: B 301 LYS cc_start: 0.8524 (mtpp) cc_final: 0.8301 (mtpp) REVERT: B 336 LEU cc_start: 0.7730 (mt) cc_final: 0.7459 (mm) REVERT: G 15 LEU cc_start: 0.8750 (mt) cc_final: 0.8466 (mt) REVERT: G 18 GLN cc_start: 0.8306 (tp40) cc_final: 0.7367 (tp40) REVERT: G 20 LYS cc_start: 0.8624 (ptpp) cc_final: 0.8200 (ptpp) REVERT: G 21 MET cc_start: 0.7705 (tmm) cc_final: 0.7407 (tmm) outliers start: 42 outliers final: 27 residues processed: 305 average time/residue: 0.2671 time to fit residues: 105.0165 Evaluate side-chains 306 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 275 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1021 CYS Chi-restraints excluded: chain A residue 1329 GLN Chi-restraints excluded: chain A residue 1362 ASP Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1514 GLU Chi-restraints excluded: chain A residue 1582 MET Chi-restraints excluded: chain A residue 1611 LYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 69 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 749 GLN ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9202 Z= 0.209 Angle : 0.614 8.267 12445 Z= 0.314 Chirality : 0.043 0.169 1392 Planarity : 0.004 0.055 1621 Dihedral : 4.908 28.353 1257 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.67 % Allowed : 21.41 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.72 (0.25), residues: 1137 helix: 1.18 (0.27), residues: 382 sheet: -1.34 (0.30), residues: 247 loop : -1.27 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 297 HIS 0.006 0.001 HIS B 311 PHE 0.028 0.002 PHE A 637 TYR 0.019 0.001 TYR B 145 ARG 0.006 0.000 ARG A1361 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 293 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 MET cc_start: 0.6863 (tpp) cc_final: 0.6603 (mmm) REVERT: A 513 LYS cc_start: 0.8229 (mtmt) cc_final: 0.8002 (mtmt) REVERT: A 530 LYS cc_start: 0.8480 (pttt) cc_final: 0.8149 (ptpp) REVERT: A 540 LYS cc_start: 0.7807 (tptt) cc_final: 0.7463 (tptp) REVERT: A 547 LYS cc_start: 0.7784 (tptm) cc_final: 0.7089 (tppt) REVERT: A 555 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6983 (mp10) REVERT: A 561 ARG cc_start: 0.8292 (mtp85) cc_final: 0.7677 (mtp180) REVERT: A 563 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 574 ASN cc_start: 0.7485 (m110) cc_final: 0.6923 (m110) REVERT: A 577 MET cc_start: 0.7170 (ptp) cc_final: 0.6605 (mtt) REVERT: A 587 ARG cc_start: 0.7659 (ttp-110) cc_final: 0.6970 (ttm110) REVERT: A 644 LYS cc_start: 0.8804 (mptt) cc_final: 0.8546 (mmtm) REVERT: A 658 GLU cc_start: 0.7376 (pt0) cc_final: 0.7120 (pt0) REVERT: A 683 GLU cc_start: 0.7163 (tt0) cc_final: 0.6835 (tt0) REVERT: A 696 ARG cc_start: 0.7303 (mtt-85) cc_final: 0.6990 (mtt-85) REVERT: A 705 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7768 (mptt) REVERT: A 723 ILE cc_start: 0.8389 (mt) cc_final: 0.8109 (mm) REVERT: A 777 ARG cc_start: 0.7651 (ptp-170) cc_final: 0.7394 (ptp90) REVERT: A 796 GLN cc_start: 0.7988 (pt0) cc_final: 0.7410 (pt0) REVERT: A 852 GLU cc_start: 0.7155 (pt0) cc_final: 0.6575 (pt0) REVERT: A 858 GLU cc_start: 0.7138 (pp20) cc_final: 0.6642 (pt0) REVERT: A 872 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7421 (mtpp) REVERT: A 874 VAL cc_start: 0.8547 (t) cc_final: 0.8243 (m) REVERT: A 882 LEU cc_start: 0.8313 (tp) cc_final: 0.7958 (tp) REVERT: A 939 GLU cc_start: 0.7954 (tp30) cc_final: 0.7707 (tp30) REVERT: A 1019 GLN cc_start: 0.7478 (tt0) cc_final: 0.7055 (tt0) REVERT: A 1020 HIS cc_start: 0.7529 (m-70) cc_final: 0.7203 (m-70) REVERT: A 1326 ILE cc_start: 0.8228 (pt) cc_final: 0.7953 (tt) REVERT: A 1327 PHE cc_start: 0.7883 (t80) cc_final: 0.7593 (t80) REVERT: A 1338 PHE cc_start: 0.7608 (t80) cc_final: 0.7322 (t80) REVERT: A 1340 GLU cc_start: 0.6599 (tp30) cc_final: 0.6299 (tp30) REVERT: A 1343 LEU cc_start: 0.8192 (mp) cc_final: 0.7980 (mm) REVERT: A 1353 ASN cc_start: 0.7624 (m110) cc_final: 0.7157 (m110) REVERT: A 1358 GLU cc_start: 0.6866 (tt0) cc_final: 0.6522 (tt0) REVERT: A 1366 LYS cc_start: 0.8492 (pttp) cc_final: 0.8107 (ttpp) REVERT: A 1405 GLU cc_start: 0.6591 (tp30) cc_final: 0.5998 (tp30) REVERT: A 1428 TYR cc_start: 0.7748 (m-10) cc_final: 0.7340 (m-10) REVERT: A 1431 GLU cc_start: 0.6775 (tm-30) cc_final: 0.6319 (tm-30) REVERT: A 1491 GLN cc_start: 0.7615 (tp-100) cc_final: 0.7186 (tm-30) REVERT: A 1503 GLN cc_start: 0.7735 (tp40) cc_final: 0.7100 (mm-40) REVERT: A 1507 LYS cc_start: 0.8261 (mttt) cc_final: 0.7847 (mttp) REVERT: A 1546 MET cc_start: 0.7568 (tpp) cc_final: 0.7247 (tpp) REVERT: A 1614 MET cc_start: 0.7933 (tpt) cc_final: 0.7594 (tpt) REVERT: A 1632 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7583 (mtmm) REVERT: A 1648 TYR cc_start: 0.7518 (m-80) cc_final: 0.7179 (m-80) REVERT: B 8 ARG cc_start: 0.8315 (mtt90) cc_final: 0.8009 (mtt90) REVERT: B 14 LEU cc_start: 0.8399 (mt) cc_final: 0.8084 (mt) REVERT: B 15 LYS cc_start: 0.8873 (mttp) cc_final: 0.8608 (mttp) REVERT: B 61 MET cc_start: 0.7530 (ppp) cc_final: 0.7144 (ptm) REVERT: B 79 LEU cc_start: 0.8462 (mt) cc_final: 0.8242 (mt) REVERT: B 118 ASP cc_start: 0.7058 (t0) cc_final: 0.6753 (t0) REVERT: B 145 TYR cc_start: 0.7857 (p90) cc_final: 0.7367 (p90) REVERT: B 146 LEU cc_start: 0.8517 (tt) cc_final: 0.8146 (tp) REVERT: B 156 GLN cc_start: 0.7654 (mt0) cc_final: 0.7429 (mt0) REVERT: B 168 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7681 (tt) REVERT: B 188 MET cc_start: 0.6445 (mmm) cc_final: 0.5873 (mmm) REVERT: B 219 ARG cc_start: 0.7341 (mtp180) cc_final: 0.7133 (ttp-170) REVERT: B 247 ASP cc_start: 0.7375 (t70) cc_final: 0.6665 (t0) REVERT: B 251 ARG cc_start: 0.7484 (mtt-85) cc_final: 0.6906 (mpp80) REVERT: B 279 SER cc_start: 0.8466 (m) cc_final: 0.8228 (t) REVERT: B 289 TYR cc_start: 0.8300 (m-80) cc_final: 0.7962 (m-80) REVERT: B 336 LEU cc_start: 0.7597 (mt) cc_final: 0.7296 (mm) REVERT: G 15 LEU cc_start: 0.8749 (mt) cc_final: 0.8476 (mt) REVERT: G 18 GLN cc_start: 0.8262 (tp40) cc_final: 0.6943 (tp-100) REVERT: G 20 LYS cc_start: 0.8574 (ptpp) cc_final: 0.8222 (ptpp) REVERT: G 21 MET cc_start: 0.7714 (tmm) cc_final: 0.7486 (tmm) REVERT: G 22 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7476 (mt-10) outliers start: 36 outliers final: 22 residues processed: 311 average time/residue: 0.2610 time to fit residues: 106.6751 Evaluate side-chains 291 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 268 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1021 CYS Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1514 GLU Chi-restraints excluded: chain A residue 1582 MET Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.0270 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.0070 chunk 94 optimal weight: 0.0070 chunk 76 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 overall best weight: 0.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN A 749 GLN A 770 HIS A 868 HIS ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 GLN A1381 GLN A1429 HIS A1606 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9202 Z= 0.169 Angle : 0.623 8.694 12445 Z= 0.313 Chirality : 0.042 0.158 1392 Planarity : 0.004 0.058 1621 Dihedral : 4.686 28.443 1257 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.28 % Allowed : 22.12 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.45 (0.25), residues: 1137 helix: 1.51 (0.27), residues: 380 sheet: -1.21 (0.30), residues: 259 loop : -1.17 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 297 HIS 0.006 0.001 HIS A 790 PHE 0.019 0.001 PHE A 637 TYR 0.022 0.001 TYR A1446 ARG 0.007 0.001 ARG A1361 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 280 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 511 MET cc_start: 0.6840 (tpp) cc_final: 0.6581 (mmm) REVERT: A 530 LYS cc_start: 0.8482 (pttt) cc_final: 0.8120 (ptpp) REVERT: A 540 LYS cc_start: 0.7767 (tptt) cc_final: 0.7566 (tptt) REVERT: A 547 LYS cc_start: 0.7701 (tptm) cc_final: 0.7014 (tppt) REVERT: A 553 LEU cc_start: 0.8533 (mp) cc_final: 0.8210 (mm) REVERT: A 561 ARG cc_start: 0.8253 (mtp85) cc_final: 0.7815 (mmt180) REVERT: A 563 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7072 (mt-10) REVERT: A 574 ASN cc_start: 0.7476 (m110) cc_final: 0.6992 (m110) REVERT: A 577 MET cc_start: 0.7226 (ptp) cc_final: 0.6700 (mtt) REVERT: A 587 ARG cc_start: 0.7546 (ttp-110) cc_final: 0.7014 (mtm110) REVERT: A 625 ARG cc_start: 0.6848 (ptp-110) cc_final: 0.6445 (ptp90) REVERT: A 658 GLU cc_start: 0.7337 (pt0) cc_final: 0.7037 (pt0) REVERT: A 683 GLU cc_start: 0.7110 (tt0) cc_final: 0.6764 (tt0) REVERT: A 696 ARG cc_start: 0.7311 (mtt-85) cc_final: 0.7021 (mtt-85) REVERT: A 723 ILE cc_start: 0.8294 (mt) cc_final: 0.8072 (mm) REVERT: A 777 ARG cc_start: 0.7631 (ptp-170) cc_final: 0.7429 (mtm180) REVERT: A 780 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6235 (pp20) REVERT: A 796 GLN cc_start: 0.7940 (pt0) cc_final: 0.7360 (pt0) REVERT: A 858 GLU cc_start: 0.7032 (pp20) cc_final: 0.6683 (tt0) REVERT: A 872 LYS cc_start: 0.7782 (mtmm) cc_final: 0.7291 (mtpp) REVERT: A 882 LEU cc_start: 0.8326 (tp) cc_final: 0.7979 (tp) REVERT: A 1019 GLN cc_start: 0.7479 (tt0) cc_final: 0.7064 (tt0) REVERT: A 1326 ILE cc_start: 0.8208 (pt) cc_final: 0.7943 (tt) REVERT: A 1327 PHE cc_start: 0.7822 (t80) cc_final: 0.7545 (t80) REVERT: A 1338 PHE cc_start: 0.7437 (t80) cc_final: 0.7175 (t80) REVERT: A 1340 GLU cc_start: 0.6389 (tp30) cc_final: 0.6089 (tp30) REVERT: A 1353 ASN cc_start: 0.7426 (m110) cc_final: 0.6799 (m-40) REVERT: A 1358 GLU cc_start: 0.6843 (tt0) cc_final: 0.6496 (tt0) REVERT: A 1366 LYS cc_start: 0.8437 (pttp) cc_final: 0.7995 (ttpp) REVERT: A 1405 GLU cc_start: 0.6592 (tp30) cc_final: 0.6010 (tp30) REVERT: A 1428 TYR cc_start: 0.7678 (m-10) cc_final: 0.7377 (m-10) REVERT: A 1431 GLU cc_start: 0.6720 (tm-30) cc_final: 0.6274 (tm-30) REVERT: A 1491 GLN cc_start: 0.7602 (tp-100) cc_final: 0.7153 (tm-30) REVERT: A 1503 GLN cc_start: 0.7697 (tp40) cc_final: 0.7019 (mm-40) REVERT: A 1507 LYS cc_start: 0.8234 (mttt) cc_final: 0.7825 (mttp) REVERT: A 1546 MET cc_start: 0.7544 (tpp) cc_final: 0.7219 (tpp) REVERT: A 1565 ILE cc_start: 0.8389 (mt) cc_final: 0.8032 (mm) REVERT: A 1579 GLN cc_start: 0.6775 (pm20) cc_final: 0.6573 (pm20) REVERT: A 1596 LEU cc_start: 0.7295 (tp) cc_final: 0.7004 (tp) REVERT: A 1598 GLN cc_start: 0.7275 (mt0) cc_final: 0.7067 (mt0) REVERT: A 1614 MET cc_start: 0.7858 (tpt) cc_final: 0.7568 (tpt) REVERT: A 1632 LYS cc_start: 0.8058 (mtmt) cc_final: 0.7518 (mtmm) REVERT: B 8 ARG cc_start: 0.8322 (mtt90) cc_final: 0.8121 (mtt90) REVERT: B 15 LYS cc_start: 0.8921 (mttp) cc_final: 0.8640 (mttp) REVERT: B 61 MET cc_start: 0.7470 (ppp) cc_final: 0.7138 (ptm) REVERT: B 79 LEU cc_start: 0.8424 (mt) cc_final: 0.8201 (mt) REVERT: B 118 ASP cc_start: 0.6751 (t0) cc_final: 0.6528 (t0) REVERT: B 145 TYR cc_start: 0.7797 (p90) cc_final: 0.7422 (p90) REVERT: B 168 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7477 (tt) REVERT: B 177 THR cc_start: 0.7122 (OUTLIER) cc_final: 0.6897 (p) REVERT: B 188 MET cc_start: 0.6318 (mmm) cc_final: 0.5782 (mmm) REVERT: B 247 ASP cc_start: 0.7358 (t70) cc_final: 0.6664 (t0) REVERT: B 251 ARG cc_start: 0.7308 (mtt-85) cc_final: 0.6981 (tpp80) REVERT: B 260 GLU cc_start: 0.6769 (tt0) cc_final: 0.6433 (tt0) REVERT: B 279 SER cc_start: 0.8441 (m) cc_final: 0.8169 (t) REVERT: B 289 TYR cc_start: 0.8284 (m-80) cc_final: 0.7926 (m-80) REVERT: B 336 LEU cc_start: 0.7533 (mt) cc_final: 0.7257 (mm) REVERT: G 15 LEU cc_start: 0.8739 (mt) cc_final: 0.8460 (mt) REVERT: G 18 GLN cc_start: 0.8186 (tp40) cc_final: 0.6837 (tp-100) REVERT: G 20 LYS cc_start: 0.8601 (ptpp) cc_final: 0.8368 (ptpp) REVERT: G 21 MET cc_start: 0.7743 (tmm) cc_final: 0.7458 (tmm) REVERT: G 22 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7391 (mt-10) outliers start: 42 outliers final: 27 residues processed: 300 average time/residue: 0.2599 time to fit residues: 101.4012 Evaluate side-chains 292 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 262 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1021 CYS Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1451 LEU Chi-restraints excluded: chain A residue 1488 ASP Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain A residue 1514 GLU Chi-restraints excluded: chain A residue 1571 LEU Chi-restraints excluded: chain A residue 1582 MET Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.0000 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 GLN A 749 GLN ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 HIS ** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 GLN A1381 GLN A1606 HIS B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9202 Z= 0.244 Angle : 0.651 9.527 12445 Z= 0.330 Chirality : 0.044 0.165 1392 Planarity : 0.004 0.049 1621 Dihedral : 4.701 30.015 1257 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.79 % Allowed : 23.55 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.40 (0.25), residues: 1137 helix: 1.49 (0.27), residues: 386 sheet: -1.16 (0.30), residues: 259 loop : -1.13 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 297 HIS 0.005 0.001 HIS A 790 PHE 0.032 0.002 PHE A 637 TYR 0.021 0.001 TYR A 534 ARG 0.008 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 259 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 511 MET cc_start: 0.6836 (tpp) cc_final: 0.6608 (mmm) REVERT: A 513 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7734 (mtpt) REVERT: A 530 LYS cc_start: 0.8481 (pttt) cc_final: 0.8139 (ptpp) REVERT: A 534 TYR cc_start: 0.7022 (t80) cc_final: 0.6345 (t80) REVERT: A 535 HIS cc_start: 0.8028 (m90) cc_final: 0.7642 (m90) REVERT: A 540 LYS cc_start: 0.7776 (tptt) cc_final: 0.7473 (tptp) REVERT: A 547 LYS cc_start: 0.7778 (tptm) cc_final: 0.7086 (tppt) REVERT: A 550 ASP cc_start: 0.7068 (t0) cc_final: 0.6668 (t0) REVERT: A 553 LEU cc_start: 0.8602 (mp) cc_final: 0.8301 (mm) REVERT: A 561 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7791 (mmt180) REVERT: A 563 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7099 (mt-10) REVERT: A 577 MET cc_start: 0.7191 (ptp) cc_final: 0.6613 (mtt) REVERT: A 587 ARG cc_start: 0.7636 (ttp-110) cc_final: 0.7088 (mtm110) REVERT: A 625 ARG cc_start: 0.6788 (ptp-110) cc_final: 0.6507 (ptp90) REVERT: A 658 GLU cc_start: 0.7321 (pt0) cc_final: 0.7076 (pt0) REVERT: A 683 GLU cc_start: 0.7200 (tt0) cc_final: 0.6897 (tt0) REVERT: A 699 ARG cc_start: 0.7203 (mtt90) cc_final: 0.6913 (mtt90) REVERT: A 723 ILE cc_start: 0.8333 (mt) cc_final: 0.8125 (mm) REVERT: A 777 ARG cc_start: 0.7668 (ptp-170) cc_final: 0.7333 (mtm180) REVERT: A 780 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6028 (pp20) REVERT: A 796 GLN cc_start: 0.8052 (pt0) cc_final: 0.7482 (pt0) REVERT: A 858 GLU cc_start: 0.7114 (pp20) cc_final: 0.6705 (tt0) REVERT: A 872 LYS cc_start: 0.7777 (mtmm) cc_final: 0.7383 (mtpp) REVERT: A 977 MET cc_start: 0.6389 (ptp) cc_final: 0.5818 (ppp) REVERT: A 1019 GLN cc_start: 0.7518 (tt0) cc_final: 0.7158 (tt0) REVERT: A 1326 ILE cc_start: 0.8248 (pt) cc_final: 0.7972 (tt) REVERT: A 1327 PHE cc_start: 0.7894 (t80) cc_final: 0.7560 (t80) REVERT: A 1338 PHE cc_start: 0.7526 (t80) cc_final: 0.7132 (t80) REVERT: A 1340 GLU cc_start: 0.6535 (tp30) cc_final: 0.6201 (tp30) REVERT: A 1343 LEU cc_start: 0.8150 (mp) cc_final: 0.7923 (mm) REVERT: A 1353 ASN cc_start: 0.7495 (m110) cc_final: 0.6853 (m-40) REVERT: A 1358 GLU cc_start: 0.6894 (tt0) cc_final: 0.6559 (tt0) REVERT: A 1366 LYS cc_start: 0.8477 (pttp) cc_final: 0.8049 (ttpp) REVERT: A 1405 GLU cc_start: 0.6599 (tp30) cc_final: 0.6007 (tp30) REVERT: A 1431 GLU cc_start: 0.6767 (tm-30) cc_final: 0.6342 (tm-30) REVERT: A 1469 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8789 (p) REVERT: A 1491 GLN cc_start: 0.7567 (tp-100) cc_final: 0.7118 (tm-30) REVERT: A 1496 GLN cc_start: 0.7590 (mt0) cc_final: 0.7315 (tt0) REVERT: A 1503 GLN cc_start: 0.7692 (tp40) cc_final: 0.7001 (mm-40) REVERT: A 1507 LYS cc_start: 0.8275 (mttt) cc_final: 0.7867 (mttp) REVERT: A 1532 LEU cc_start: 0.8043 (tp) cc_final: 0.7793 (tt) REVERT: A 1546 MET cc_start: 0.7597 (tpp) cc_final: 0.7267 (tpp) REVERT: A 1565 ILE cc_start: 0.8446 (mt) cc_final: 0.8036 (mm) REVERT: A 1596 LEU cc_start: 0.7347 (tp) cc_final: 0.7072 (tp) REVERT: A 1606 HIS cc_start: 0.8036 (m170) cc_final: 0.7828 (m170) REVERT: A 1622 LYS cc_start: 0.7960 (mttp) cc_final: 0.7477 (mptt) REVERT: A 1632 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7625 (mtmm) REVERT: B 15 LYS cc_start: 0.8932 (mttp) cc_final: 0.8652 (mttp) REVERT: B 79 LEU cc_start: 0.8470 (mt) cc_final: 0.8251 (mt) REVERT: B 118 ASP cc_start: 0.6856 (t0) cc_final: 0.6614 (t0) REVERT: B 145 TYR cc_start: 0.7834 (p90) cc_final: 0.7464 (p90) REVERT: B 168 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7572 (tt) REVERT: B 177 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.7009 (p) REVERT: B 188 MET cc_start: 0.6384 (mmm) cc_final: 0.5823 (mmm) REVERT: B 247 ASP cc_start: 0.7424 (t70) cc_final: 0.6723 (t0) REVERT: B 251 ARG cc_start: 0.7361 (mtt-85) cc_final: 0.6953 (tpp80) REVERT: B 260 GLU cc_start: 0.6818 (tt0) cc_final: 0.6466 (tt0) REVERT: B 279 SER cc_start: 0.8441 (m) cc_final: 0.8170 (t) REVERT: B 289 TYR cc_start: 0.8326 (m-80) cc_final: 0.8012 (m-80) REVERT: B 336 LEU cc_start: 0.7549 (mt) cc_final: 0.7294 (mm) REVERT: G 15 LEU cc_start: 0.8756 (mt) cc_final: 0.8472 (mt) REVERT: G 18 GLN cc_start: 0.8248 (tp40) cc_final: 0.6709 (tp-100) REVERT: G 20 LYS cc_start: 0.8617 (ptpp) cc_final: 0.8355 (ptpp) REVERT: G 21 MET cc_start: 0.7772 (tmm) cc_final: 0.7485 (tmm) REVERT: G 22 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7493 (mt-10) outliers start: 47 outliers final: 39 residues processed: 283 average time/residue: 0.2655 time to fit residues: 97.7133 Evaluate side-chains 296 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 253 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1021 CYS Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1453 SER Chi-restraints excluded: chain A residue 1469 THR Chi-restraints excluded: chain A residue 1488 ASP Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1513 LEU Chi-restraints excluded: chain A residue 1514 GLU Chi-restraints excluded: chain A residue 1571 LEU Chi-restraints excluded: chain A residue 1582 MET Chi-restraints excluded: chain A residue 1593 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 GLN A 749 GLN ** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 GLN A1381 GLN A1598 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9202 Z= 0.216 Angle : 0.647 9.760 12445 Z= 0.324 Chirality : 0.043 0.169 1392 Planarity : 0.004 0.048 1621 Dihedral : 4.712 30.156 1257 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.20 % Allowed : 23.75 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1137 helix: 1.51 (0.27), residues: 389 sheet: -1.14 (0.31), residues: 259 loop : -1.10 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 297 HIS 0.006 0.001 HIS A 790 PHE 0.033 0.002 PHE A 637 TYR 0.019 0.001 TYR A 534 ARG 0.007 0.001 ARG A1361 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 259 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7582 (tt) REVERT: A 530 LYS cc_start: 0.8486 (pttt) cc_final: 0.8162 (ptpp) REVERT: A 540 LYS cc_start: 0.7771 (tptt) cc_final: 0.7438 (tptp) REVERT: A 547 LYS cc_start: 0.7739 (tptm) cc_final: 0.7075 (tppt) REVERT: A 550 ASP cc_start: 0.7049 (t70) cc_final: 0.6615 (t0) REVERT: A 553 LEU cc_start: 0.8585 (mp) cc_final: 0.8284 (mm) REVERT: A 563 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7066 (mt-10) REVERT: A 577 MET cc_start: 0.7188 (ptp) cc_final: 0.6622 (mtt) REVERT: A 587 ARG cc_start: 0.7613 (ttp-110) cc_final: 0.6887 (ttm110) REVERT: A 658 GLU cc_start: 0.7327 (pt0) cc_final: 0.7108 (pt0) REVERT: A 673 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6584 (mm-30) REVERT: A 683 GLU cc_start: 0.7224 (tt0) cc_final: 0.6943 (tt0) REVERT: A 777 ARG cc_start: 0.7640 (ptp-170) cc_final: 0.7344 (mtm180) REVERT: A 780 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6019 (pp20) REVERT: A 796 GLN cc_start: 0.7889 (pt0) cc_final: 0.7526 (pt0) REVERT: A 852 GLU cc_start: 0.7015 (pt0) cc_final: 0.6540 (pm20) REVERT: A 858 GLU cc_start: 0.7106 (pp20) cc_final: 0.6693 (tt0) REVERT: A 872 LYS cc_start: 0.7733 (mtmm) cc_final: 0.7395 (mtpp) REVERT: A 882 LEU cc_start: 0.8334 (tp) cc_final: 0.7928 (tp) REVERT: A 1326 ILE cc_start: 0.8236 (pt) cc_final: 0.7968 (tt) REVERT: A 1338 PHE cc_start: 0.7475 (t80) cc_final: 0.7256 (t80) REVERT: A 1340 GLU cc_start: 0.6489 (tp30) cc_final: 0.6137 (tp30) REVERT: A 1353 ASN cc_start: 0.7560 (m110) cc_final: 0.6941 (m-40) REVERT: A 1358 GLU cc_start: 0.6910 (tt0) cc_final: 0.6523 (tt0) REVERT: A 1366 LYS cc_start: 0.8483 (pttp) cc_final: 0.8037 (ttpp) REVERT: A 1405 GLU cc_start: 0.6588 (tp30) cc_final: 0.6330 (tp30) REVERT: A 1431 GLU cc_start: 0.6777 (tm-30) cc_final: 0.6340 (tm-30) REVERT: A 1472 LEU cc_start: 0.7929 (mt) cc_final: 0.7651 (tp) REVERT: A 1491 GLN cc_start: 0.7605 (tp-100) cc_final: 0.7145 (tm-30) REVERT: A 1496 GLN cc_start: 0.7576 (mt0) cc_final: 0.7302 (tt0) REVERT: A 1503 GLN cc_start: 0.7734 (tp40) cc_final: 0.7040 (mm-40) REVERT: A 1507 LYS cc_start: 0.8282 (mttt) cc_final: 0.7857 (mttp) REVERT: A 1532 LEU cc_start: 0.8043 (tp) cc_final: 0.7794 (tt) REVERT: A 1546 MET cc_start: 0.7568 (tpp) cc_final: 0.7323 (mpp) REVERT: A 1565 ILE cc_start: 0.8320 (mt) cc_final: 0.8039 (mm) REVERT: A 1594 VAL cc_start: 0.7549 (OUTLIER) cc_final: 0.6998 (t) REVERT: A 1596 LEU cc_start: 0.7334 (tp) cc_final: 0.7056 (tp) REVERT: A 1598 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.7046 (mt0) REVERT: A 1614 MET cc_start: 0.7893 (tpt) cc_final: 0.7434 (tpt) REVERT: A 1622 LYS cc_start: 0.7962 (mttp) cc_final: 0.7569 (mtpt) REVERT: A 1632 LYS cc_start: 0.8169 (mtmt) cc_final: 0.7631 (mtmm) REVERT: B 15 LYS cc_start: 0.8923 (mttp) cc_final: 0.8644 (mttp) REVERT: B 61 MET cc_start: 0.7503 (ppp) cc_final: 0.7188 (ptm) REVERT: B 79 LEU cc_start: 0.8462 (mt) cc_final: 0.8244 (mt) REVERT: B 118 ASP cc_start: 0.6826 (t0) cc_final: 0.6573 (t0) REVERT: B 145 TYR cc_start: 0.7828 (p90) cc_final: 0.7472 (p90) REVERT: B 168 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7585 (tt) REVERT: B 177 THR cc_start: 0.7171 (OUTLIER) cc_final: 0.6955 (p) REVERT: B 188 MET cc_start: 0.6380 (mmm) cc_final: 0.5810 (mmm) REVERT: B 247 ASP cc_start: 0.7426 (t70) cc_final: 0.6738 (t0) REVERT: B 251 ARG cc_start: 0.7324 (mtt-85) cc_final: 0.6931 (tpp80) REVERT: B 260 GLU cc_start: 0.6803 (tt0) cc_final: 0.6469 (tt0) REVERT: B 279 SER cc_start: 0.8447 (m) cc_final: 0.8185 (t) REVERT: B 289 TYR cc_start: 0.8308 (m-80) cc_final: 0.7989 (m-80) REVERT: B 336 LEU cc_start: 0.7517 (mt) cc_final: 0.7227 (mm) REVERT: G 15 LEU cc_start: 0.8760 (mt) cc_final: 0.8474 (mt) REVERT: G 18 GLN cc_start: 0.8203 (tp40) cc_final: 0.6675 (tp-100) REVERT: G 20 LYS cc_start: 0.8590 (ptpp) cc_final: 0.8308 (ptpp) REVERT: G 21 MET cc_start: 0.7764 (tmm) cc_final: 0.7479 (tmm) REVERT: G 22 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7383 (mt-10) outliers start: 51 outliers final: 36 residues processed: 280 average time/residue: 0.2699 time to fit residues: 98.6773 Evaluate side-chains 299 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 257 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1021 CYS Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1488 ASP Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1514 GLU Chi-restraints excluded: chain A residue 1582 MET Chi-restraints excluded: chain A residue 1594 VAL Chi-restraints excluded: chain A residue 1598 GLN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.0000 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.0050 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN A 559 GLN A 749 GLN ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 GLN A1381 GLN A1598 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9202 Z= 0.197 Angle : 0.646 10.263 12445 Z= 0.323 Chirality : 0.043 0.178 1392 Planarity : 0.004 0.048 1621 Dihedral : 4.700 31.855 1257 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.38 % Allowed : 24.87 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.24 (0.26), residues: 1137 helix: 1.60 (0.27), residues: 387 sheet: -1.04 (0.31), residues: 263 loop : -1.04 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 297 HIS 0.005 0.001 HIS A 790 PHE 0.015 0.001 PHE A 593 TYR 0.016 0.001 TYR A1428 ARG 0.009 0.001 ARG A1361 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 261 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 LYS cc_start: 0.8443 (pttt) cc_final: 0.8113 (ptpp) REVERT: A 534 TYR cc_start: 0.7068 (t80) cc_final: 0.6460 (t80) REVERT: A 535 HIS cc_start: 0.7995 (m90) cc_final: 0.7750 (m90) REVERT: A 540 LYS cc_start: 0.7761 (tptt) cc_final: 0.7422 (tptp) REVERT: A 547 LYS cc_start: 0.7717 (tptm) cc_final: 0.7031 (tppt) REVERT: A 550 ASP cc_start: 0.6988 (t70) cc_final: 0.6609 (t0) REVERT: A 553 LEU cc_start: 0.8548 (mp) cc_final: 0.8257 (mm) REVERT: A 561 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7690 (mmm160) REVERT: A 563 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7101 (mt-10) REVERT: A 577 MET cc_start: 0.7156 (ptp) cc_final: 0.6607 (mtt) REVERT: A 587 ARG cc_start: 0.7557 (ttp-110) cc_final: 0.6998 (mtm110) REVERT: A 640 GLU cc_start: 0.7128 (tp30) cc_final: 0.6883 (tp30) REVERT: A 658 GLU cc_start: 0.7316 (pt0) cc_final: 0.7089 (pt0) REVERT: A 683 GLU cc_start: 0.7219 (tt0) cc_final: 0.6936 (tt0) REVERT: A 699 ARG cc_start: 0.7259 (mtt90) cc_final: 0.6839 (mtm-85) REVERT: A 777 ARG cc_start: 0.7629 (ptp-170) cc_final: 0.7348 (mtm180) REVERT: A 780 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6089 (pp20) REVERT: A 796 GLN cc_start: 0.8133 (pt0) cc_final: 0.7595 (pt0) REVERT: A 852 GLU cc_start: 0.7027 (pt0) cc_final: 0.6497 (pm20) REVERT: A 858 GLU cc_start: 0.7069 (pp20) cc_final: 0.6670 (tt0) REVERT: A 872 LYS cc_start: 0.7754 (mtmm) cc_final: 0.7443 (mtpp) REVERT: A 939 GLU cc_start: 0.7875 (tp30) cc_final: 0.7673 (tp30) REVERT: A 1019 GLN cc_start: 0.7378 (tt0) cc_final: 0.7098 (tm-30) REVERT: A 1326 ILE cc_start: 0.8221 (pt) cc_final: 0.7952 (tt) REVERT: A 1327 PHE cc_start: 0.7871 (t80) cc_final: 0.7537 (t80) REVERT: A 1340 GLU cc_start: 0.6494 (tp30) cc_final: 0.6128 (tp30) REVERT: A 1353 ASN cc_start: 0.7544 (m110) cc_final: 0.6934 (m-40) REVERT: A 1358 GLU cc_start: 0.6980 (tt0) cc_final: 0.6611 (tt0) REVERT: A 1361 ARG cc_start: 0.7472 (ttt-90) cc_final: 0.6961 (tmt170) REVERT: A 1366 LYS cc_start: 0.8472 (pttp) cc_final: 0.8018 (ttpp) REVERT: A 1405 GLU cc_start: 0.6593 (tp30) cc_final: 0.6336 (tp30) REVERT: A 1431 GLU cc_start: 0.6771 (tm-30) cc_final: 0.6348 (tm-30) REVERT: A 1472 LEU cc_start: 0.7890 (mt) cc_final: 0.7642 (tp) REVERT: A 1491 GLN cc_start: 0.7603 (tp-100) cc_final: 0.7107 (tm-30) REVERT: A 1496 GLN cc_start: 0.7544 (mt0) cc_final: 0.7280 (tt0) REVERT: A 1503 GLN cc_start: 0.7728 (tp40) cc_final: 0.7034 (mm-40) REVERT: A 1507 LYS cc_start: 0.8278 (mttt) cc_final: 0.7855 (mttp) REVERT: A 1532 LEU cc_start: 0.8047 (tp) cc_final: 0.7799 (tt) REVERT: A 1546 MET cc_start: 0.7535 (tpp) cc_final: 0.7285 (mpp) REVERT: A 1565 ILE cc_start: 0.8363 (mt) cc_final: 0.8047 (mm) REVERT: A 1594 VAL cc_start: 0.7489 (t) cc_final: 0.6987 (t) REVERT: A 1596 LEU cc_start: 0.7278 (tp) cc_final: 0.7043 (tp) REVERT: A 1598 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.6890 (mt0) REVERT: A 1614 MET cc_start: 0.7893 (tpt) cc_final: 0.7462 (tpt) REVERT: A 1622 LYS cc_start: 0.7893 (mttp) cc_final: 0.7528 (mtpt) REVERT: A 1632 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7548 (mtmm) REVERT: B 15 LYS cc_start: 0.8927 (mttp) cc_final: 0.8654 (mttp) REVERT: B 61 MET cc_start: 0.7496 (ppp) cc_final: 0.7175 (ptm) REVERT: B 79 LEU cc_start: 0.8491 (mt) cc_final: 0.8282 (mt) REVERT: B 118 ASP cc_start: 0.6790 (t0) cc_final: 0.6535 (t0) REVERT: B 145 TYR cc_start: 0.7799 (p90) cc_final: 0.7468 (p90) REVERT: B 168 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7590 (tt) REVERT: B 188 MET cc_start: 0.6356 (mmm) cc_final: 0.5794 (mmm) REVERT: B 247 ASP cc_start: 0.7440 (t70) cc_final: 0.6763 (t0) REVERT: B 251 ARG cc_start: 0.7323 (mtt-85) cc_final: 0.6926 (tpp80) REVERT: B 260 GLU cc_start: 0.6815 (tt0) cc_final: 0.6475 (tt0) REVERT: B 279 SER cc_start: 0.8437 (m) cc_final: 0.8169 (t) REVERT: B 289 TYR cc_start: 0.8278 (m-80) cc_final: 0.7919 (m-80) REVERT: B 336 LEU cc_start: 0.7505 (mt) cc_final: 0.7218 (mm) REVERT: G 15 LEU cc_start: 0.8757 (mt) cc_final: 0.8474 (mt) REVERT: G 18 GLN cc_start: 0.8167 (tp40) cc_final: 0.7197 (tp40) REVERT: G 20 LYS cc_start: 0.8581 (ptpp) cc_final: 0.8295 (ptpp) REVERT: G 21 MET cc_start: 0.7759 (tmm) cc_final: 0.7429 (tmm) outliers start: 43 outliers final: 35 residues processed: 279 average time/residue: 0.2825 time to fit residues: 103.2292 Evaluate side-chains 293 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 255 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1021 CYS Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1488 ASP Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain A residue 1499 GLU Chi-restraints excluded: chain A residue 1513 LEU Chi-restraints excluded: chain A residue 1514 GLU Chi-restraints excluded: chain A residue 1593 SER Chi-restraints excluded: chain A residue 1598 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.2980 chunk 67 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 66 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN A 749 GLN ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 GLN A1381 GLN A1598 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9202 Z= 0.220 Angle : 0.664 10.474 12445 Z= 0.331 Chirality : 0.043 0.185 1392 Planarity : 0.004 0.066 1621 Dihedral : 4.695 32.788 1257 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.18 % Allowed : 25.28 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.22 (0.26), residues: 1137 helix: 1.62 (0.27), residues: 387 sheet: -1.04 (0.31), residues: 262 loop : -1.02 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 297 HIS 0.004 0.001 HIS A 790 PHE 0.033 0.002 PHE A 637 TYR 0.016 0.001 TYR A1428 ARG 0.015 0.001 ARG A1361 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 256 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 LYS cc_start: 0.8446 (pttt) cc_final: 0.8122 (ptpp) REVERT: A 534 TYR cc_start: 0.7055 (t80) cc_final: 0.6316 (t80) REVERT: A 535 HIS cc_start: 0.7990 (m90) cc_final: 0.7738 (m90) REVERT: A 540 LYS cc_start: 0.7757 (tptt) cc_final: 0.7424 (tptp) REVERT: A 547 LYS cc_start: 0.7738 (tptm) cc_final: 0.7076 (tppt) REVERT: A 550 ASP cc_start: 0.7001 (t70) cc_final: 0.6614 (t0) REVERT: A 553 LEU cc_start: 0.8544 (mp) cc_final: 0.8251 (mm) REVERT: A 561 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7704 (mmm160) REVERT: A 563 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7085 (mt-10) REVERT: A 577 MET cc_start: 0.7183 (ptp) cc_final: 0.6602 (mtt) REVERT: A 587 ARG cc_start: 0.7603 (ttp-110) cc_final: 0.7062 (mtm110) REVERT: A 640 GLU cc_start: 0.7135 (tp30) cc_final: 0.6885 (tp30) REVERT: A 668 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7601 (tt) REVERT: A 683 GLU cc_start: 0.7241 (tt0) cc_final: 0.6947 (tt0) REVERT: A 699 ARG cc_start: 0.7283 (mtt90) cc_final: 0.6939 (mtm-85) REVERT: A 777 ARG cc_start: 0.7648 (ptp-170) cc_final: 0.7375 (mtm180) REVERT: A 780 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6109 (pp20) REVERT: A 796 GLN cc_start: 0.8154 (pt0) cc_final: 0.7606 (pt0) REVERT: A 852 GLU cc_start: 0.7094 (pt0) cc_final: 0.6613 (pm20) REVERT: A 858 GLU cc_start: 0.7089 (pp20) cc_final: 0.6685 (tt0) REVERT: A 872 LYS cc_start: 0.7729 (mtmm) cc_final: 0.7414 (mtpp) REVERT: A 882 LEU cc_start: 0.8336 (tp) cc_final: 0.7958 (tp) REVERT: A 939 GLU cc_start: 0.7875 (tp30) cc_final: 0.7660 (tp30) REVERT: A 1019 GLN cc_start: 0.7555 (tt0) cc_final: 0.6921 (tm-30) REVERT: A 1326 ILE cc_start: 0.8237 (pt) cc_final: 0.7979 (tt) REVERT: A 1340 GLU cc_start: 0.6525 (tp30) cc_final: 0.6092 (tp30) REVERT: A 1353 ASN cc_start: 0.7589 (m110) cc_final: 0.6966 (m-40) REVERT: A 1358 GLU cc_start: 0.6995 (tt0) cc_final: 0.6598 (tt0) REVERT: A 1366 LYS cc_start: 0.8487 (pttp) cc_final: 0.8045 (ttpp) REVERT: A 1405 GLU cc_start: 0.6552 (tp30) cc_final: 0.6257 (tp30) REVERT: A 1431 GLU cc_start: 0.6782 (tm-30) cc_final: 0.6355 (tm-30) REVERT: A 1472 LEU cc_start: 0.7901 (mt) cc_final: 0.7647 (tp) REVERT: A 1496 GLN cc_start: 0.7561 (mt0) cc_final: 0.7300 (tt0) REVERT: A 1503 GLN cc_start: 0.7745 (tp40) cc_final: 0.7041 (mm-40) REVERT: A 1507 LYS cc_start: 0.8285 (mttt) cc_final: 0.7854 (mttp) REVERT: A 1532 LEU cc_start: 0.8054 (tp) cc_final: 0.7803 (tt) REVERT: A 1546 MET cc_start: 0.7551 (tpp) cc_final: 0.7290 (mpp) REVERT: A 1565 ILE cc_start: 0.8367 (mt) cc_final: 0.8055 (mm) REVERT: A 1594 VAL cc_start: 0.7413 (t) cc_final: 0.6975 (t) REVERT: A 1596 LEU cc_start: 0.7303 (tp) cc_final: 0.7084 (tp) REVERT: A 1598 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6915 (mt0) REVERT: A 1614 MET cc_start: 0.7885 (tpt) cc_final: 0.7460 (tpt) REVERT: A 1622 LYS cc_start: 0.7820 (mttp) cc_final: 0.7562 (mtpt) REVERT: A 1632 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7643 (mtmm) REVERT: B 15 LYS cc_start: 0.8927 (mttp) cc_final: 0.8661 (mttp) REVERT: B 61 MET cc_start: 0.7519 (ppp) cc_final: 0.7191 (ptm) REVERT: B 79 LEU cc_start: 0.8498 (mt) cc_final: 0.8286 (mt) REVERT: B 118 ASP cc_start: 0.6822 (t0) cc_final: 0.6558 (t0) REVERT: B 145 TYR cc_start: 0.7815 (p90) cc_final: 0.7490 (p90) REVERT: B 168 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7850 (tt) REVERT: B 188 MET cc_start: 0.6371 (mmm) cc_final: 0.5820 (mmm) REVERT: B 247 ASP cc_start: 0.7453 (t70) cc_final: 0.6785 (t0) REVERT: B 279 SER cc_start: 0.8432 (m) cc_final: 0.8178 (t) REVERT: B 289 TYR cc_start: 0.8293 (m-80) cc_final: 0.7921 (m-80) REVERT: B 336 LEU cc_start: 0.7529 (mt) cc_final: 0.7232 (mm) REVERT: G 15 LEU cc_start: 0.8766 (mt) cc_final: 0.8481 (mt) REVERT: G 18 GLN cc_start: 0.8044 (tp40) cc_final: 0.7058 (tp40) REVERT: G 20 LYS cc_start: 0.8614 (ptpp) cc_final: 0.8398 (ptpp) REVERT: G 21 MET cc_start: 0.7802 (tmm) cc_final: 0.7443 (tmm) outliers start: 41 outliers final: 34 residues processed: 275 average time/residue: 0.2606 time to fit residues: 93.2842 Evaluate side-chains 286 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 248 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1021 CYS Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1488 ASP Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain A residue 1514 GLU Chi-restraints excluded: chain A residue 1571 LEU Chi-restraints excluded: chain A residue 1598 GLN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 104 optimal weight: 0.0470 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 0.0970 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN A 749 GLN ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 GLN A1381 GLN A1598 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9202 Z= 0.210 Angle : 0.661 10.826 12445 Z= 0.329 Chirality : 0.043 0.195 1392 Planarity : 0.004 0.049 1621 Dihedral : 4.664 33.020 1257 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.98 % Allowed : 25.59 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.22 (0.26), residues: 1137 helix: 1.60 (0.27), residues: 387 sheet: -1.07 (0.31), residues: 262 loop : -0.98 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 297 HIS 0.004 0.001 HIS A 790 PHE 0.034 0.002 PHE A 637 TYR 0.018 0.001 TYR A1428 ARG 0.008 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 256 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 LYS cc_start: 0.8428 (pttt) cc_final: 0.8096 (ptpp) REVERT: A 534 TYR cc_start: 0.7115 (t80) cc_final: 0.6625 (t80) REVERT: A 540 LYS cc_start: 0.7753 (tptt) cc_final: 0.7419 (tptp) REVERT: A 547 LYS cc_start: 0.7715 (tptm) cc_final: 0.7062 (tppt) REVERT: A 550 ASP cc_start: 0.6977 (t70) cc_final: 0.6617 (t0) REVERT: A 553 LEU cc_start: 0.8531 (mp) cc_final: 0.8243 (mm) REVERT: A 561 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7710 (mmm160) REVERT: A 563 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7071 (mt-10) REVERT: A 577 MET cc_start: 0.7166 (ptp) cc_final: 0.6619 (mtt) REVERT: A 587 ARG cc_start: 0.7554 (ttp-110) cc_final: 0.7013 (mtm110) REVERT: A 640 GLU cc_start: 0.7117 (tp30) cc_final: 0.6867 (tp30) REVERT: A 668 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7597 (tt) REVERT: A 672 ASN cc_start: 0.8167 (t0) cc_final: 0.7803 (m-40) REVERT: A 699 ARG cc_start: 0.7286 (mtt90) cc_final: 0.6777 (mtm-85) REVERT: A 777 ARG cc_start: 0.7642 (ptp-170) cc_final: 0.7378 (mtm180) REVERT: A 780 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6111 (pp20) REVERT: A 796 GLN cc_start: 0.8164 (pt0) cc_final: 0.7621 (pt0) REVERT: A 852 GLU cc_start: 0.7125 (pt0) cc_final: 0.6643 (pm20) REVERT: A 858 GLU cc_start: 0.7072 (pp20) cc_final: 0.6666 (tt0) REVERT: A 872 LYS cc_start: 0.7621 (mtmm) cc_final: 0.7348 (mtpp) REVERT: A 882 LEU cc_start: 0.8333 (tp) cc_final: 0.7954 (tp) REVERT: A 939 GLU cc_start: 0.7899 (tp30) cc_final: 0.7673 (tp30) REVERT: A 977 MET cc_start: 0.6321 (ptp) cc_final: 0.6106 (ptp) REVERT: A 1019 GLN cc_start: 0.7554 (tt0) cc_final: 0.6904 (tm-30) REVERT: A 1326 ILE cc_start: 0.8232 (pt) cc_final: 0.7978 (tt) REVERT: A 1338 PHE cc_start: 0.7665 (t80) cc_final: 0.7402 (t80) REVERT: A 1340 GLU cc_start: 0.6498 (tp30) cc_final: 0.6127 (tp30) REVERT: A 1353 ASN cc_start: 0.7599 (m110) cc_final: 0.6966 (m-40) REVERT: A 1358 GLU cc_start: 0.6996 (tt0) cc_final: 0.6618 (tt0) REVERT: A 1366 LYS cc_start: 0.8450 (pttp) cc_final: 0.8037 (ttpp) REVERT: A 1405 GLU cc_start: 0.6525 (tp30) cc_final: 0.6246 (tp30) REVERT: A 1431 GLU cc_start: 0.6773 (tm-30) cc_final: 0.6352 (tm-30) REVERT: A 1472 LEU cc_start: 0.7882 (mt) cc_final: 0.7631 (tp) REVERT: A 1473 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7482 (mt-10) REVERT: A 1496 GLN cc_start: 0.7548 (mt0) cc_final: 0.7287 (tt0) REVERT: A 1503 GLN cc_start: 0.7741 (tp40) cc_final: 0.7035 (mm-40) REVERT: A 1507 LYS cc_start: 0.8284 (mttt) cc_final: 0.7864 (mttp) REVERT: A 1532 LEU cc_start: 0.8054 (tp) cc_final: 0.7802 (tt) REVERT: A 1546 MET cc_start: 0.7525 (tpp) cc_final: 0.7246 (mpp) REVERT: A 1565 ILE cc_start: 0.8304 (mt) cc_final: 0.8042 (mm) REVERT: A 1594 VAL cc_start: 0.7459 (t) cc_final: 0.7007 (t) REVERT: A 1598 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6928 (mt0) REVERT: A 1614 MET cc_start: 0.7854 (tpt) cc_final: 0.7411 (tpt) REVERT: A 1622 LYS cc_start: 0.7781 (mttp) cc_final: 0.7566 (mtpt) REVERT: A 1632 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7640 (mtmm) REVERT: B 15 LYS cc_start: 0.8915 (mttp) cc_final: 0.8656 (mttp) REVERT: B 61 MET cc_start: 0.7509 (ppp) cc_final: 0.7195 (ptm) REVERT: B 79 LEU cc_start: 0.8487 (mt) cc_final: 0.8275 (mt) REVERT: B 118 ASP cc_start: 0.6786 (t0) cc_final: 0.6529 (t0) REVERT: B 145 TYR cc_start: 0.7810 (p90) cc_final: 0.7498 (p90) REVERT: B 188 MET cc_start: 0.6354 (mmm) cc_final: 0.5806 (mmm) REVERT: B 247 ASP cc_start: 0.7455 (t70) cc_final: 0.6783 (t0) REVERT: B 251 ARG cc_start: 0.7363 (mtt-85) cc_final: 0.6980 (tpp80) REVERT: B 279 SER cc_start: 0.8431 (m) cc_final: 0.8180 (t) REVERT: B 289 TYR cc_start: 0.8289 (m-80) cc_final: 0.7937 (m-80) REVERT: B 336 LEU cc_start: 0.7520 (mt) cc_final: 0.7238 (mm) REVERT: G 15 LEU cc_start: 0.8766 (mt) cc_final: 0.8485 (mt) REVERT: G 18 GLN cc_start: 0.8028 (tp40) cc_final: 0.7073 (tp40) REVERT: G 20 LYS cc_start: 0.8617 (ptpp) cc_final: 0.8395 (ptpp) REVERT: G 21 MET cc_start: 0.7808 (tmm) cc_final: 0.7449 (tmm) outliers start: 39 outliers final: 33 residues processed: 275 average time/residue: 0.2620 time to fit residues: 94.5152 Evaluate side-chains 286 residues out of total 981 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 250 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 970 THR Chi-restraints excluded: chain A residue 1021 CYS Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1025 MET Chi-restraints excluded: chain A residue 1370 GLN Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1407 ASP Chi-restraints excluded: chain A residue 1410 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1488 ASP Chi-restraints excluded: chain A residue 1489 LEU Chi-restraints excluded: chain A residue 1513 LEU Chi-restraints excluded: chain A residue 1514 GLU Chi-restraints excluded: chain A residue 1571 LEU Chi-restraints excluded: chain A residue 1598 GLN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 25 optimal weight: 0.0570 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.0070 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 HIS A 559 GLN A 749 GLN ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 GLN A1381 GLN A1598 GLN ** B 259 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 = 0.4058 r_free = 0.4058 target = 0.158256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.136264 restraints weight = 11852.326| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.67 r_work: 0.3630 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9202 Z= 0.194 Angle : 0.666 11.117 12445 Z= 0.330 Chirality : 0.043 0.193 1392 Planarity : 0.004 0.049 1621 Dihedral : 4.636 32.817 1257 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.98 % Allowed : 25.79 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.21 (0.26), residues: 1137 helix: 1.59 (0.27), residues: 387 sheet: -1.07 (0.31), residues: 263 loop : -0.96 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 297 HIS 0.013 0.001 HIS A 535 PHE 0.034 0.002 PHE A 637 TYR 0.016 0.001 TYR A1428 ARG 0.008 0.001 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2785.42 seconds wall clock time: 50 minutes 29.29 seconds (3029.29 seconds total)