Starting phenix.real_space_refine on Thu Mar 14 21:32:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eei_31077/03_2024/7eei_31077.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eei_31077/03_2024/7eei_31077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eei_31077/03_2024/7eei_31077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eei_31077/03_2024/7eei_31077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eei_31077/03_2024/7eei_31077.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eei_31077/03_2024/7eei_31077.pdb" } resolution = 3.6 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= 0.001 sd= 0.004 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 6290 2.51 5 N 1723 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A ASP 337": not complete - not flipped Residue "A ASP 409": "OD1" <-> "OD2" Residue "A ASP 444": not complete - not flipped Residue "A GLU 452": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "A ASP 640": not complete - not flipped Residue "A GLU 684": "OE1" <-> "OE2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "A GLU 702": not complete - not flipped Residue "A ARG 713": "NH1" <-> "NH2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A GLU 814": "OE1" <-> "OE2" Residue "A GLU 849": "OE1" <-> "OE2" Residue "A GLU 890": "OE1" <-> "OE2" Residue "A ARG 904": "NH1" <-> "NH2" Residue "A GLU 1079": "OE1" <-> "OE2" Residue "A GLU 1102": "OE1" <-> "OE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1187": "OE1" <-> "OE2" Residue "A GLU 1216": "OE1" <-> "OE2" Residue "A GLU 1376": "OE1" <-> "OE2" Residue "A GLU 1435": "OE1" <-> "OE2" Residue "A ARG 1505": "NH1" <-> "NH2" Residue "A PHE 1546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1551": "OE1" <-> "OE2" Residue "A GLU 1565": "OE1" <-> "OE2" 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: 9825 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1400, 9825 Classifications: {'peptide': 1400} Incomplete info: {'backbone_only': 48, 'n_c_alpha_c_only': 14, 'truncation_to_alanine': 250} Link IDs: {'PTRANS': 58, 'TRANS': 1341} Unresolved chain links: 1 Unresolved chain link angles: 29 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1425 Unresolved non-hydrogen angles: 1855 Unresolved non-hydrogen dihedrals: 1090 Unresolved non-hydrogen chiralities: 161 Planarities with less than four sites: {'GLN:plan1': 18, 'HIS:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 4, 'ASP:plan': 46, 'PHE:plan': 14, 'GLU:plan': 64, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 799 Time building chain proxies: 5.31, per 1000 atoms: 0.54 Number of scatterers: 9825 At special positions: 0 Unit cell: (87.48, 112.32, 95.04, 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 1747 8.00 N 1723 7.00 C 6290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 986 " - pdb=" SG CYS A1159 " distance=2.04 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: 3.81 Conformation dependent library (CDL) restraints added in 2.0 seconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2532 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 7 sheets defined 53.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 215 through 228 Processing helix chain 'A' and resid 231 through 239 removed outlier: 3.794A pdb=" N THR A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 253 removed outlier: 3.505A pdb=" N PHE A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 280 removed outlier: 3.674A pdb=" N ILE A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 311 removed outlier: 3.757A pdb=" N TYR A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 381 through 391 removed outlier: 3.952A pdb=" N ALA A 385 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 439 removed outlier: 3.678A pdb=" N GLN A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 457 removed outlier: 3.791A pdb=" N CYS A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.647A pdb=" N LEU A 472 " --> pdb=" O TYR A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 497 through 506 Processing helix chain 'A' and resid 507 through 530 removed outlier: 4.629A pdb=" N TRP A 513 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 608 removed outlier: 3.682A pdb=" N THR A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN A 605 " --> pdb=" O SER A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 624 Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 640 through 659 Processing helix chain 'A' and resid 661 through 677 removed outlier: 3.527A pdb=" N GLU A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG A 672 " --> pdb=" O GLN A 668 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR A 673 " --> pdb=" O THR A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.501A pdb=" N SER A 693 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 695 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 721 Processing helix chain 'A' and resid 748 through 756 removed outlier: 3.682A pdb=" N LEU A 752 " --> pdb=" O ASP A 748 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYS A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 785 removed outlier: 4.081A pdb=" N LYS A 779 " --> pdb=" O GLY A 775 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE A 780 " --> pdb=" O MET A 776 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 781 " --> pdb=" O TYR A 777 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 783 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS A 785 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 828 Processing helix chain 'A' and resid 830 through 846 removed outlier: 3.692A pdb=" N ILE A 839 " --> pdb=" O ILE A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 852 removed outlier: 3.569A pdb=" N LEU A 851 " --> pdb=" O THR A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 871 Processing helix chain 'A' and resid 880 through 889 Processing helix chain 'A' and resid 894 through 910 removed outlier: 4.736A pdb=" N ASP A 901 " --> pdb=" O GLN A 897 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 904 " --> pdb=" O GLU A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 952 Processing helix chain 'A' and resid 960 through 979 removed outlier: 3.700A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Proline residue: A 968 - end of helix removed outlier: 4.540A pdb=" N GLY A 972 " --> pdb=" O PRO A 968 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1012 removed outlier: 3.573A pdb=" N PHE A1011 " --> pdb=" O MET A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1015 No H-bonds generated for 'chain 'A' and resid 1013 through 1015' Processing helix chain 'A' and resid 1016 through 1029 removed outlier: 4.088A pdb=" N ARG A1029 " --> pdb=" O SER A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1044 removed outlier: 3.825A pdb=" N GLY A1044 " --> pdb=" O LYS A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1063 Processing helix chain 'A' and resid 1089 through 1116 removed outlier: 3.793A pdb=" N SER A1106 " --> pdb=" O GLU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1121 removed outlier: 4.239A pdb=" N SER A1121 " --> pdb=" O PRO A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1164 removed outlier: 3.805A pdb=" N LYS A1163 " --> pdb=" O CYS A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1207 Processing helix chain 'A' and resid 1219 through 1235 Processing helix chain 'A' and resid 1238 through 1257 Processing helix chain 'A' and resid 1263 through 1275 removed outlier: 3.829A pdb=" N GLU A1267 " --> pdb=" O GLU A1263 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS A1270 " --> pdb=" O LEU A1266 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A1271 " --> pdb=" O GLU A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1281 Processing helix chain 'A' and resid 1295 through 1307 Processing helix chain 'A' and resid 1308 through 1316 Processing helix chain 'A' and resid 1358 through 1368 Processing helix chain 'A' and resid 1374 through 1380 removed outlier: 4.159A pdb=" N ILE A1378 " --> pdb=" O TRP A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1384 Processing helix chain 'A' and resid 1391 through 1404 Processing helix chain 'A' and resid 1409 through 1414 Processing helix chain 'A' and resid 1416 through 1427 removed outlier: 3.520A pdb=" N LYS A1420 " --> pdb=" O ASN A1416 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A1425 " --> pdb=" O VAL A1421 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1457 Processing helix chain 'A' and resid 1459 through 1469 removed outlier: 4.531A pdb=" N GLU A1469 " --> pdb=" O PHE A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1496 removed outlier: 3.607A pdb=" N ILE A1496 " --> pdb=" O LYS A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1510 Processing helix chain 'A' and resid 1518 through 1530 Proline residue: A1525 - end of helix removed outlier: 3.888A pdb=" N LEU A1528 " --> pdb=" O SER A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1559 Processing helix chain 'A' and resid 1574 through 1582 Processing helix chain 'A' and resid 1976 through 1989 removed outlier: 4.110A pdb=" N SER A1980 " --> pdb=" O ASN A1976 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 416 through 418 removed outlier: 4.230A pdb=" N ALA A 416 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 537 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 416 through 418 removed outlier: 4.230A pdb=" N ALA A 416 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 537 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 724 through 727 Processing sheet with id=AA4, first strand: chain 'A' and resid 856 through 857 Processing sheet with id=AA5, first strand: chain 'A' and resid 928 through 931 removed outlier: 7.293A pdb=" N ILE A 914 " --> pdb=" O MET A1033 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1192 through 1194 Processing sheet with id=AA7, first strand: chain 'A' and resid 1490 through 1491 509 hydrogen bonds defined for protein. 1464 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: 3.67 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3136 1.34 - 1.47: 2541 1.47 - 1.60: 4265 1.60 - 1.73: 1 1.73 - 1.86: 95 Bond restraints: 10038 Sorted by residual: bond pdb=" CB PHE A 495 " pdb=" CG PHE A 495 " ideal model delta sigma weight residual 1.502 1.600 -0.098 2.30e-02 1.89e+03 1.80e+01 bond pdb=" N GLU A1165 " pdb=" CA GLU A1165 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.15e-02 7.56e+03 1.50e+01 bond pdb=" CA PHE A 495 " pdb=" CB PHE A 495 " ideal model delta sigma weight residual 1.527 1.571 -0.044 1.44e-02 4.82e+03 9.32e+00 bond pdb=" N VAL A1421 " pdb=" CA VAL A1421 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.16e+00 bond pdb=" C GLY A 494 " pdb=" N PHE A 495 " ideal model delta sigma weight residual 1.331 1.368 -0.037 1.26e-02 6.30e+03 8.76e+00 ... (remaining 10033 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.21: 275 106.21 - 113.24: 5205 113.24 - 120.27: 4055 120.27 - 127.30: 3925 127.30 - 134.33: 134 Bond angle restraints: 13594 Sorted by residual: angle pdb=" N PHE A 495 " pdb=" CA PHE A 495 " pdb=" C PHE A 495 " ideal model delta sigma weight residual 110.19 101.16 9.03 1.24e+00 6.50e-01 5.31e+01 angle pdb=" CA PHE A 495 " pdb=" C PHE A 495 " pdb=" N ASN A 496 " ideal model delta sigma weight residual 115.58 126.50 -10.92 1.55e+00 4.16e-01 4.96e+01 angle pdb=" CA PHE A 495 " pdb=" C PHE A 495 " pdb=" O PHE A 495 " ideal model delta sigma weight residual 122.01 116.20 5.81 1.05e+00 9.07e-01 3.06e+01 angle pdb=" N SER A 323 " pdb=" CA SER A 323 " pdb=" C SER A 323 " ideal model delta sigma weight residual 110.35 118.09 -7.74 1.40e+00 5.10e-01 3.06e+01 angle pdb=" C SER A 322 " pdb=" N SER A 323 " pdb=" CA SER A 323 " ideal model delta sigma weight residual 121.31 129.15 -7.84 1.49e+00 4.50e-01 2.77e+01 ... (remaining 13589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.67: 5620 22.67 - 45.35: 240 45.35 - 68.02: 43 68.02 - 90.70: 7 90.70 - 113.37: 2 Dihedral angle restraints: 5912 sinusoidal: 1949 harmonic: 3963 Sorted by residual: dihedral pdb=" CA ASP A 574 " pdb=" C ASP A 574 " pdb=" N LEU A 575 " pdb=" CA LEU A 575 " ideal model delta harmonic sigma weight residual 180.00 123.42 56.58 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA SER A 322 " pdb=" C SER A 322 " pdb=" N SER A 323 " pdb=" CA SER A 323 " ideal model delta harmonic sigma weight residual -180.00 -126.77 -53.23 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CB CYS A 986 " pdb=" SG CYS A 986 " pdb=" SG CYS A1159 " pdb=" CB CYS A1159 " ideal model delta sinusoidal sigma weight residual -86.00 -160.07 74.07 1 1.00e+01 1.00e-02 6.96e+01 ... (remaining 5909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1203 0.065 - 0.129: 265 0.129 - 0.194: 48 0.194 - 0.259: 6 0.259 - 0.323: 3 Chirality restraints: 1525 Sorted by residual: chirality pdb=" CB ILE A 781 " pdb=" CA ILE A 781 " pdb=" CG1 ILE A 781 " pdb=" CG2 ILE A 781 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA PHE A 495 " pdb=" N PHE A 495 " pdb=" C PHE A 495 " pdb=" CB PHE A 495 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ILE A 325 " pdb=" N ILE A 325 " pdb=" C ILE A 325 " pdb=" CB ILE A 325 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 1522 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 573 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C PHE A 573 " 0.055 2.00e-02 2.50e+03 pdb=" O PHE A 573 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP A 574 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1563 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO A1564 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A1564 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1564 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 495 " -0.015 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C PHE A 495 " 0.048 2.00e-02 2.50e+03 pdb=" O PHE A 495 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 496 " -0.017 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 46 2.56 - 3.15: 8266 3.15 - 3.73: 15368 3.73 - 4.32: 20314 4.32 - 4.90: 33823 Nonbonded interactions: 77817 Sorted by model distance: nonbonded pdb=" O ASN A 960 " pdb=" OD1 ASN A 960 " model vdw 1.975 3.040 nonbonded pdb=" NE2 GLN A 483 " pdb=" CD1 PHE A 495 " model vdw 1.992 3.420 nonbonded pdb=" NE2 GLN A 483 " pdb=" CE1 PHE A 495 " model vdw 2.169 3.420 nonbonded pdb=" O ALA A 792 " pdb=" N LYS A 797 " model vdw 2.228 2.520 nonbonded pdb=" NZ LYS A 339 " pdb=" O VAL A1261 " model vdw 2.237 2.520 ... (remaining 77812 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 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: 1.360 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 29.910 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 0.098 10038 Z= 0.422 Angle : 1.090 12.610 13594 Z= 0.627 Chirality : 0.057 0.323 1525 Planarity : 0.007 0.070 1748 Dihedral : 13.713 113.372 3377 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.22 % 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: -1.90 (0.20), residues: 1396 helix: -0.33 (0.19), residues: 653 sheet: -2.60 (0.53), residues: 65 loop : -2.08 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1275 HIS 0.011 0.002 HIS A 913 PHE 0.045 0.003 PHE A 495 TYR 0.020 0.003 TYR A1169 ARG 0.004 0.001 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A 602 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 248 ASP cc_start: 0.8281 (m-30) cc_final: 0.8063 (m-30) REVERT: A 700 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7403 (mmm160) REVERT: A 727 LYS cc_start: 0.5501 (tttt) cc_final: 0.5108 (mttt) REVERT: A 757 TYR cc_start: 0.8378 (m-80) cc_final: 0.7942 (m-80) REVERT: A 1059 PHE cc_start: 0.8636 (t80) cc_final: 0.8432 (t80) REVERT: A 1107 LEU cc_start: 0.9126 (tp) cc_final: 0.8898 (tt) REVERT: A 1187 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7860 (tm-30) REVERT: A 1580 ARG cc_start: 0.7054 (tpt170) cc_final: 0.6657 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2064 time to fit residues: 74.4002 Evaluate side-chains 183 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 0.0040 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 20.0000 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN A 785 HIS A1100 HIS A1197 GLN ** A1287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1381 ASN A1479 ASN A1570 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10038 Z= 0.182 Angle : 0.600 8.561 13594 Z= 0.313 Chirality : 0.042 0.159 1525 Planarity : 0.005 0.056 1748 Dihedral : 4.914 32.707 1473 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.79 % Allowed : 12.36 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.78 (0.22), residues: 1396 helix: 0.80 (0.20), residues: 674 sheet: -1.83 (0.58), residues: 65 loop : -1.84 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1017 HIS 0.020 0.002 HIS A1063 PHE 0.015 0.001 PHE A1239 TYR 0.016 0.002 TYR A1313 ARG 0.004 0.000 ARG A1029 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 197 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A 599 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A1040 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 258 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8100 (tm-30) REVERT: A 262 ARG cc_start: 0.8711 (ttp-170) cc_final: 0.8406 (ttp-170) REVERT: A 727 LYS cc_start: 0.5515 (tttt) cc_final: 0.5129 (mtpt) REVERT: A 901 ASP cc_start: 0.8580 (t0) cc_final: 0.8363 (m-30) REVERT: A 929 TYR cc_start: 0.8251 (m-80) cc_final: 0.7982 (m-80) outliers start: 23 outliers final: 11 residues processed: 211 average time/residue: 0.1832 time to fit residues: 57.5144 Evaluate side-chains 182 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain A residue 1256 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN A1189 ASN A1570 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10038 Z= 0.192 Angle : 0.569 8.020 13594 Z= 0.296 Chirality : 0.041 0.178 1525 Planarity : 0.005 0.055 1748 Dihedral : 4.724 39.587 1473 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.27 % Allowed : 14.67 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.22), residues: 1396 helix: 1.16 (0.20), residues: 679 sheet: -1.27 (0.62), residues: 65 loop : -1.78 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1559 HIS 0.011 0.001 HIS A1063 PHE 0.017 0.001 PHE A1059 TYR 0.012 0.001 TYR A 584 ARG 0.006 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 176 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A 599 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS A1040 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 258 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8174 (tm-30) REVERT: A 262 ARG cc_start: 0.8734 (ttp-170) cc_final: 0.8460 (ttp-170) REVERT: A 727 LYS cc_start: 0.5560 (tttt) cc_final: 0.5304 (mttt) REVERT: A 929 TYR cc_start: 0.8373 (m-80) cc_final: 0.8085 (m-80) outliers start: 27 outliers final: 17 residues processed: 194 average time/residue: 0.1777 time to fit residues: 51.6296 Evaluate side-chains 184 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1250 CYS Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1570 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 127 optimal weight: 30.0000 chunk 135 optimal weight: 0.6980 chunk 121 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 0.4980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1247 GLN A1276 ASN A1570 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10038 Z= 0.280 Angle : 0.585 6.790 13594 Z= 0.308 Chirality : 0.042 0.133 1525 Planarity : 0.005 0.057 1748 Dihedral : 4.741 40.734 1473 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.36 % Allowed : 15.88 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.20 (0.23), residues: 1396 helix: 1.32 (0.20), residues: 671 sheet: -1.05 (0.63), residues: 65 loop : -1.64 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1559 HIS 0.029 0.002 HIS A1570 PHE 0.016 0.002 PHE A 247 TYR 0.020 0.002 TYR A 867 ARG 0.003 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 1.130 Fit side-chains TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 258 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8503 (tm-30) REVERT: A 727 LYS cc_start: 0.5809 (tttt) cc_final: 0.5456 (mtpt) REVERT: A 929 TYR cc_start: 0.8506 (m-80) cc_final: 0.8124 (m-80) REVERT: A 1059 PHE cc_start: 0.8678 (t80) cc_final: 0.8476 (t80) outliers start: 36 outliers final: 26 residues processed: 187 average time/residue: 0.1780 time to fit residues: 49.8335 Evaluate side-chains 184 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain A residue 1250 CYS Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1276 ASN Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1563 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.0980 chunk 1 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 93 optimal weight: 0.0070 chunk 0 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10038 Z= 0.169 Angle : 0.539 11.889 13594 Z= 0.280 Chirality : 0.040 0.139 1525 Planarity : 0.005 0.059 1748 Dihedral : 4.466 36.609 1473 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.39 % Allowed : 17.82 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.05 (0.23), residues: 1396 helix: 1.49 (0.21), residues: 675 sheet: -0.76 (0.65), residues: 65 loop : -1.66 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1559 HIS 0.006 0.001 HIS A1253 PHE 0.013 0.001 PHE A1546 TYR 0.017 0.001 TYR A 867 ARG 0.006 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 1.171 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 727 LYS cc_start: 0.5705 (tttt) cc_final: 0.5383 (mtpt) REVERT: A 929 TYR cc_start: 0.8336 (m-80) cc_final: 0.8037 (m-80) REVERT: A 1307 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7576 (p) outliers start: 28 outliers final: 21 residues processed: 188 average time/residue: 0.1793 time to fit residues: 50.6825 Evaluate side-chains 185 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 163 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1250 CYS Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1276 ASN Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain A residue 1375 ILE Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1563 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 135 optimal weight: 0.0770 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10038 Z= 0.152 Angle : 0.523 13.070 13594 Z= 0.269 Chirality : 0.039 0.146 1525 Planarity : 0.004 0.060 1748 Dihedral : 4.156 31.696 1473 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.64 % Allowed : 18.67 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.23), residues: 1396 helix: 1.65 (0.21), residues: 676 sheet: -0.49 (0.65), residues: 65 loop : -1.65 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1559 HIS 0.007 0.001 HIS A1253 PHE 0.016 0.001 PHE A1054 TYR 0.023 0.001 TYR A 867 ARG 0.004 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 1.071 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 659 GLU cc_start: 0.8211 (tt0) cc_final: 0.7970 (tt0) REVERT: A 727 LYS cc_start: 0.5676 (tttt) cc_final: 0.5362 (mtpt) REVERT: A 1307 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7637 (p) outliers start: 30 outliers final: 23 residues processed: 192 average time/residue: 0.1686 time to fit residues: 49.3980 Evaluate side-chains 190 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1250 CYS Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain A residue 1370 ILE Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1563 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 HIS ** A1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10038 Z= 0.281 Angle : 0.587 13.624 13594 Z= 0.303 Chirality : 0.042 0.150 1525 Planarity : 0.005 0.059 1748 Dihedral : 4.506 38.096 1473 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.24 % Allowed : 18.91 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.08 (0.23), residues: 1396 helix: 1.60 (0.20), residues: 669 sheet: -0.89 (0.64), residues: 72 loop : -1.55 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1559 HIS 0.006 0.001 HIS A1253 PHE 0.018 0.002 PHE A1054 TYR 0.021 0.002 TYR A 867 ARG 0.005 0.000 ARG A1505 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 1.175 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 727 LYS cc_start: 0.6124 (tttt) cc_final: 0.5777 (mtpt) REVERT: A 1307 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7825 (p) outliers start: 35 outliers final: 25 residues processed: 180 average time/residue: 0.1684 time to fit residues: 46.2357 Evaluate side-chains 179 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 756 CYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1250 CYS Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain A residue 1370 ILE Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1563 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 0.0050 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1090 HIS ** A1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10038 Z= 0.151 Angle : 0.535 12.703 13594 Z= 0.273 Chirality : 0.039 0.141 1525 Planarity : 0.004 0.060 1748 Dihedral : 4.156 31.739 1473 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.52 % Allowed : 19.64 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.16 (0.23), residues: 1396 helix: 1.68 (0.21), residues: 676 sheet: -0.24 (0.70), residues: 61 loop : -1.62 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1328 HIS 0.007 0.001 HIS A1253 PHE 0.021 0.001 PHE A1054 TYR 0.017 0.001 TYR A 867 ARG 0.004 0.000 ARG A 850 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 1.147 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 727 LYS cc_start: 0.5958 (tttt) cc_final: 0.5650 (mtpt) REVERT: A 929 TYR cc_start: 0.8162 (m-10) cc_final: 0.7879 (m-10) REVERT: A 1102 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8560 (mm-30) REVERT: A 1307 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7711 (p) outliers start: 29 outliers final: 23 residues processed: 189 average time/residue: 0.1699 time to fit residues: 48.6417 Evaluate side-chains 190 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1250 CYS Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1563 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.0470 chunk 125 optimal weight: 0.0270 chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 132 optimal weight: 0.2980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10038 Z= 0.147 Angle : 0.531 13.147 13594 Z= 0.268 Chirality : 0.039 0.143 1525 Planarity : 0.004 0.062 1748 Dihedral : 3.977 28.805 1473 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.39 % Allowed : 20.61 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1396 helix: 1.80 (0.21), residues: 675 sheet: -0.09 (0.70), residues: 61 loop : -1.64 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A1559 HIS 0.008 0.001 HIS A1253 PHE 0.024 0.001 PHE A1054 TYR 0.019 0.001 TYR A 867 ARG 0.004 0.000 ARG A 904 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 0.905 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 236 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8252 (mm-30) REVERT: A 727 LYS cc_start: 0.5936 (tttt) cc_final: 0.5653 (mtpt) REVERT: A 902 CYS cc_start: 0.8637 (m) cc_final: 0.8141 (m) REVERT: A 969 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7722 (mm-30) REVERT: A 1102 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8569 (mm-30) REVERT: A 1193 TYR cc_start: 0.7904 (m-80) cc_final: 0.7654 (m-80) REVERT: A 1307 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7782 (p) outliers start: 28 outliers final: 23 residues processed: 190 average time/residue: 0.1683 time to fit residues: 48.4421 Evaluate side-chains 190 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 756 CYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain A residue 1027 PHE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1250 CYS Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1563 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 139 optimal weight: 20.0000 chunk 128 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10038 Z= 0.187 Angle : 0.552 13.571 13594 Z= 0.280 Chirality : 0.040 0.136 1525 Planarity : 0.004 0.061 1748 Dihedral : 4.065 30.071 1473 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.27 % Allowed : 21.21 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.26 (0.23), residues: 1396 helix: 1.82 (0.21), residues: 675 sheet: -0.27 (0.68), residues: 61 loop : -1.64 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1559 HIS 0.013 0.001 HIS A1253 PHE 0.016 0.001 PHE A1546 TYR 0.019 0.001 TYR A 867 ARG 0.005 0.000 ARG A 850 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.028 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP A 586 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET A1586 " (corrupted residue). Skipping it. REVERT: A 236 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8225 (mm-30) REVERT: A 727 LYS cc_start: 0.5959 (tttt) cc_final: 0.5653 (mtpt) REVERT: A 902 CYS cc_start: 0.8656 (m) cc_final: 0.8178 (m) REVERT: A 1102 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8596 (mm-30) REVERT: A 1162 MET cc_start: 0.8644 (tmm) cc_final: 0.8346 (ttt) REVERT: A 1307 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7804 (p) outliers start: 27 outliers final: 25 residues processed: 182 average time/residue: 0.1731 time to fit residues: 48.0932 Evaluate side-chains 190 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 535 ASN Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 756 CYS Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 785 HIS Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1013 SER Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1183 ASP Chi-restraints excluded: chain A residue 1250 CYS Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1307 THR Chi-restraints excluded: chain A residue 1453 LEU Chi-restraints excluded: chain A residue 1521 LEU Chi-restraints excluded: chain A residue 1563 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 30 optimal weight: 0.3980 chunk 111 optimal weight: 8.9990 chunk 46 optimal weight: 0.0570 chunk 114 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 97 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.120561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099137 restraints weight = 19839.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102158 restraints weight = 9843.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.104136 restraints weight = 6215.175| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10038 Z= 0.151 Angle : 0.547 13.405 13594 Z= 0.273 Chirality : 0.040 0.237 1525 Planarity : 0.004 0.062 1748 Dihedral : 3.944 26.812 1473 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.27 % Allowed : 21.45 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1396 helix: 1.83 (0.21), residues: 675 sheet: -0.05 (0.70), residues: 61 loop : -1.65 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 462 HIS 0.014 0.001 HIS A1253 PHE 0.022 0.001 PHE A1301 TYR 0.020 0.001 TYR A 867 ARG 0.005 0.000 ARG A 850 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1965.86 seconds wall clock time: 36 minutes 4.88 seconds (2164.88 seconds total)