Starting phenix.real_space_refine on Fri Feb 16 18:37:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5t_21547/02_2024/6w5t_21547_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5t_21547/02_2024/6w5t_21547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5t_21547/02_2024/6w5t_21547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5t_21547/02_2024/6w5t_21547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5t_21547/02_2024/6w5t_21547_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5t_21547/02_2024/6w5t_21547_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6688 atoms to isotropic. 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 71 5.16 5 C 6156 2.51 5 N 1496 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A GLU 713": "OE1" <-> "OE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A ARG 978": "NH1" <-> "NH2" Residue "A ARG 980": "NH1" <-> "NH2" Residue "A ARG 989": "NH1" <-> "NH2" Residue "A ARG 997": "NH1" <-> "NH2" Residue "A GLU 1089": "OE1" <-> "OE2" Residue "A GLU 1166": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9505 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9189 Classifications: {'peptide': 1175} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1111} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 182 Unusual residues: {'CLR': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.82, per 1000 atoms: 0.61 Number of scatterers: 9505 At special positions: 0 Unit cell: (103.602, 91.348, 152.618, 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 71 16.00 O 1782 8.00 N 1496 7.00 C 6156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=1.51 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.04 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.05 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.06 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.04 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.97 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 979 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 976 " distance=2.03 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 Links applied ALPHA1-3 " NAG C 2 " - " MAN C 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1401 " - " ASN A 452 " " NAG A1402 " - " ASN A 459 " " NAG A1405 " - " ASN A 524 " " NAG A1409 " - " ASN A 598 " " NAG A1410 " - " ASN A 916 " " NAG A1414 " - " ASN A 961 " " NAG A1415 " - " ASN A 968 " " NAG A1416 " - " ASN A1064 " " NAG A1419 " - " ASN A 158 " " NAG B 1 " - " ASN A 478 " " NAG C 1 " - " ASN A 557 " " NAG D 1 " - " ASN A 931 " " NAG E 1 " - " ASN A 222 " Time building additional restraints: 4.95 Conformation dependent library (CDL) restraints added in 2.3 seconds 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 5 sheets defined 51.8% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.761A pdb=" N GLN A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix removed outlier: 4.904A pdb=" N ARG A 96 " --> pdb=" O GLN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 removed outlier: 3.608A pdb=" N ASN A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 removed outlier: 3.542A pdb=" N PHE A 120 " --> pdb=" O GLN A 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 186 through 194 removed outlier: 4.043A pdb=" N ILE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 269 through 294 removed outlier: 3.991A pdb=" N ALA A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 348 removed outlier: 4.051A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 370 removed outlier: 4.900A pdb=" N GLY A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU A 368 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N VAL A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N PHE A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 387 through 398 Processing helix chain 'A' and resid 437 through 452 removed outlier: 3.520A pdb=" N ASN A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 467 No H-bonds generated for 'chain 'A' and resid 464 through 467' Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 509 through 518 removed outlier: 3.510A pdb=" N ARG A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 575 through 593 removed outlier: 3.652A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 616 Processing helix chain 'A' and resid 621 through 638 removed outlier: 4.106A pdb=" N ILE A 626 " --> pdb=" O PHE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 678 Processing helix chain 'A' and resid 686 through 710 Proline residue: A 691 - end of helix Processing helix chain 'A' and resid 721 through 749 Proline residue: A 733 - end of helix Processing helix chain 'A' and resid 755 through 788 Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.634A pdb=" N PHE A 820 " --> pdb=" O CYS A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 829 No H-bonds generated for 'chain 'A' and resid 826 through 829' Processing helix chain 'A' and resid 834 through 851 Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 871 through 882 Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 942 through 950 Processing helix chain 'A' and resid 984 through 987 No H-bonds generated for 'chain 'A' and resid 984 through 987' Processing helix chain 'A' and resid 993 through 1004 Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1048 through 1069 Processing helix chain 'A' and resid 1083 through 1088 removed outlier: 4.119A pdb=" N VAL A1086 " --> pdb=" O VAL A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1094 through 1116 Processing helix chain 'A' and resid 1121 through 1145 Processing helix chain 'A' and resid 1151 through 1176 removed outlier: 4.007A pdb=" N GLY A1162 " --> pdb=" O VAL A1158 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A1165 " --> pdb=" O CYS A1161 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A1167 " --> pdb=" O ILE A1163 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A1172 " --> pdb=" O CYS A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1201 removed outlier: 4.301A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A1200 " --> pdb=" O SER A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1213 Processing helix chain 'A' and resid 1220 through 1251 removed outlier: 4.526A pdb=" N PHE A1226 " --> pdb=" O GLN A1222 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A1244 " --> pdb=" O GLY A1240 " (cutoff:3.500A) Proline residue: A1245 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 206 through 208 removed outlier: 6.615A pdb=" N GLN A 145 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL A 123 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR A 147 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 121 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 409 through 411 Processing sheet with id= C, first strand: chain 'A' and resid 418 through 420 Processing sheet with id= D, first strand: chain 'A' and resid 1036 through 1041 removed outlier: 3.546A pdb=" N PHE A1038 " --> pdb=" O PHE A 891 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 958 through 960 408 hydrogen bonds defined for protein. 1200 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: 2.84 Time building geometry restraints manager: 5.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2947 1.35 - 1.48: 2625 1.48 - 1.61: 4081 1.61 - 1.74: 1 1.74 - 1.87: 99 Bond restraints: 9753 Sorted by residual: bond pdb=" CA CYS A 909 " pdb=" C CYS A 909 " ideal model delta sigma weight residual 1.524 1.579 -0.055 1.27e-02 6.20e+03 1.90e+01 bond pdb=" N CYS A 909 " pdb=" CA CYS A 909 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.19e-02 7.06e+03 1.47e+01 bond pdb=" CA TYR A 269 " pdb=" C TYR A 269 " ideal model delta sigma weight residual 1.522 1.473 0.049 1.39e-02 5.18e+03 1.23e+01 bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.26e+00 bond pdb=" C1 NAG A1410 " pdb=" O5 NAG A1410 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.65e+00 ... (remaining 9748 not shown) Histogram of bond angle deviations from ideal: 97.30 - 105.53: 242 105.53 - 113.76: 5604 113.76 - 121.99: 5866 121.99 - 130.22: 1546 130.22 - 138.45: 38 Bond angle restraints: 13296 Sorted by residual: angle pdb=" N CYS A 909 " pdb=" CA CYS A 909 " pdb=" C CYS A 909 " ideal model delta sigma weight residual 111.07 138.45 -27.38 1.07e+00 8.73e-01 6.55e+02 angle pdb=" N ASN A 823 " pdb=" CA ASN A 823 " pdb=" C ASN A 823 " ideal model delta sigma weight residual 111.14 121.36 -10.22 1.08e+00 8.57e-01 8.95e+01 angle pdb=" N SER A 602 " pdb=" CA SER A 602 " pdb=" C SER A 602 " ideal model delta sigma weight residual 108.41 97.30 11.11 1.63e+00 3.76e-01 4.64e+01 angle pdb=" CA CYS A 909 " pdb=" C CYS A 909 " pdb=" N GLY A 910 " ideal model delta sigma weight residual 117.07 124.47 -7.40 1.14e+00 7.69e-01 4.21e+01 angle pdb=" C GLY A 910 " pdb=" N GLY A 911 " pdb=" CA GLY A 911 " ideal model delta sigma weight residual 122.42 129.43 -7.01 1.13e+00 7.83e-01 3.85e+01 ... (remaining 13291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.95: 5696 27.95 - 55.90: 304 55.90 - 83.85: 53 83.85 - 111.80: 33 111.80 - 139.76: 13 Dihedral angle restraints: 6099 sinusoidal: 2677 harmonic: 3422 Sorted by residual: dihedral pdb=" CB CYS A 240 " pdb=" SG CYS A 240 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual -86.00 0.20 -86.20 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CA ASN A 70 " pdb=" C ASN A 70 " pdb=" N VAL A 71 " pdb=" CA VAL A 71 " ideal model delta harmonic sigma weight residual 180.00 -137.91 -42.09 0 5.00e+00 4.00e-02 7.08e+01 dihedral pdb=" CA GLY A 69 " pdb=" C GLY A 69 " pdb=" N ASN A 70 " pdb=" CA ASN A 70 " ideal model delta harmonic sigma weight residual 180.00 141.81 38.19 0 5.00e+00 4.00e-02 5.83e+01 ... (remaining 6096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.948: 1555 0.948 - 1.896: 0 1.896 - 2.844: 0 2.844 - 3.792: 0 3.792 - 4.740: 2 Chirality restraints: 1557 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 2.34 -4.74 2.00e-02 2.50e+03 5.62e+04 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 2.33 -4.73 2.00e-02 2.50e+03 5.59e+04 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.38e+02 ... (remaining 1554 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG E 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.071 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.190 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.343 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG C 2 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.048 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.344 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG E 1 " -0.088 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.077 2.00e-02 2.50e+03 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 177 2.62 - 3.19: 9648 3.19 - 3.76: 14565 3.76 - 4.33: 20284 4.33 - 4.90: 32735 Nonbonded interactions: 77409 Sorted by model distance: nonbonded pdb=" O3 NAG B 2 " pdb=" O7 NAG B 2 " model vdw 2.054 2.440 nonbonded pdb=" OH TYR A 487 " pdb=" O VAL A 541 " model vdw 2.077 2.440 nonbonded pdb=" N GLU A 30 " pdb=" OE1 GLU A 30 " model vdw 2.134 2.520 nonbonded pdb=" OD1 ASN A 459 " pdb=" N2 NAG A1402 " model vdw 2.200 2.520 nonbonded pdb=" N GLN A 716 " pdb=" OE1 GLN A 716 " model vdw 2.206 2.520 ... (remaining 77404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and resid 1 through 2) selection = (chain 'D' and resid 1 through 2) } 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.000 Extract box with map and model: 3.560 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 32.540 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.007 0.083 9753 Z= 0.456 Angle : 1.144 27.378 13296 Z= 0.714 Chirality : 0.182 4.740 1557 Planarity : 0.015 0.298 1664 Dihedral : 19.767 139.756 3854 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 48.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.97 % Favored : 91.52 % Rotamer: Outliers : 5.60 % Allowed : 8.95 % Favored : 85.45 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.22), residues: 1167 helix: -0.92 (0.20), residues: 591 sheet: -2.19 (0.58), residues: 87 loop : -2.97 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 27 HIS 0.004 0.001 HIS A1239 PHE 0.031 0.002 PHE A 747 TYR 0.018 0.002 TYR A1225 ARG 0.006 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 246 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 PRO cc_start: 0.7137 (Cg_exo) cc_final: 0.6527 (Cg_endo) REVERT: A 83 LEU cc_start: 0.8865 (tt) cc_final: 0.8662 (tt) REVERT: A 93 PHE cc_start: 0.7739 (m-80) cc_final: 0.7238 (m-80) REVERT: A 192 TYR cc_start: 0.8081 (t80) cc_final: 0.7659 (t80) REVERT: A 272 MET cc_start: 0.8537 (mmp) cc_final: 0.8332 (mmm) REVERT: A 376 ASN cc_start: 0.8793 (t0) cc_final: 0.8496 (p0) REVERT: A 406 GLU cc_start: 0.8602 (mp0) cc_final: 0.8357 (mp0) REVERT: A 498 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7105 (mttt) REVERT: A 550 TYR cc_start: 0.8108 (p90) cc_final: 0.7790 (p90) REVERT: A 612 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7890 (mm-30) REVERT: A 714 ARG cc_start: 0.6922 (pmt170) cc_final: 0.6604 (ptp90) REVERT: A 726 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8572 (ttp-110) REVERT: A 825 TYR cc_start: 0.8789 (t80) cc_final: 0.8034 (t80) REVERT: A 1053 ASP cc_start: 0.7015 (t0) cc_final: 0.6808 (t0) REVERT: A 1089 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7088 (tm-30) REVERT: A 1110 PHE cc_start: 0.8557 (t80) cc_final: 0.8330 (t80) REVERT: A 1137 ASN cc_start: 0.9151 (m110) cc_final: 0.8803 (m110) REVERT: A 1235 LEU cc_start: 0.8425 (tt) cc_final: 0.7987 (mt) outliers start: 57 outliers final: 23 residues processed: 286 average time/residue: 0.2361 time to fit residues: 92.3304 Evaluate side-chains 197 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 171 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 824 SER Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 997 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 119 GLN A 136 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN A 465 GLN A 823 ASN A1024 ASN A1137 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9753 Z= 0.247 Angle : 0.862 11.885 13296 Z= 0.410 Chirality : 0.052 0.277 1557 Planarity : 0.005 0.044 1664 Dihedral : 15.538 108.820 1844 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.26 % Favored : 93.57 % Rotamer: Outliers : 3.15 % Allowed : 17.40 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.49 (0.24), residues: 1167 helix: 0.11 (0.21), residues: 608 sheet: -2.36 (0.51), residues: 89 loop : -2.15 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 27 HIS 0.007 0.001 HIS A1042 PHE 0.020 0.002 PHE A 504 TYR 0.028 0.002 TYR A 293 ARG 0.006 0.001 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 1.076 Fit side-chains REVERT: A 78 ARG cc_start: 0.8716 (tpt-90) cc_final: 0.8452 (tpp-160) REVERT: A 127 GLU cc_start: 0.5387 (OUTLIER) cc_final: 0.4829 (pm20) REVERT: A 192 TYR cc_start: 0.8091 (t80) cc_final: 0.7802 (t80) REVERT: A 277 MET cc_start: 0.7707 (mmt) cc_final: 0.7240 (mmm) REVERT: A 288 PHE cc_start: 0.6327 (m-10) cc_final: 0.5986 (m-10) REVERT: A 415 THR cc_start: 0.7637 (m) cc_final: 0.7434 (t) REVERT: A 550 TYR cc_start: 0.7928 (p90) cc_final: 0.7686 (p90) REVERT: A 740 PHE cc_start: 0.8171 (t80) cc_final: 0.7879 (t80) REVERT: A 825 TYR cc_start: 0.8701 (t80) cc_final: 0.7975 (t80) REVERT: A 1005 ASP cc_start: 0.8789 (t0) cc_final: 0.8470 (t0) REVERT: A 1089 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7232 (tm-30) REVERT: A 1097 ASP cc_start: 0.7623 (t70) cc_final: 0.7307 (t70) REVERT: A 1106 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7939 (mp) REVERT: A 1110 PHE cc_start: 0.8553 (t80) cc_final: 0.8308 (t80) REVERT: A 1127 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7975 (tpp) REVERT: A 1137 ASN cc_start: 0.9124 (m-40) cc_final: 0.8909 (m110) REVERT: A 1168 CYS cc_start: 0.6284 (t) cc_final: 0.5566 (t) outliers start: 32 outliers final: 20 residues processed: 219 average time/residue: 0.1921 time to fit residues: 61.3643 Evaluate side-chains 184 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1127 MET Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9753 Z= 0.278 Angle : 0.795 10.729 13296 Z= 0.377 Chirality : 0.049 0.262 1557 Planarity : 0.004 0.039 1664 Dihedral : 13.511 105.213 1805 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.68 % Favored : 93.14 % Rotamer: Outliers : 5.21 % Allowed : 19.08 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.24), residues: 1167 helix: 0.53 (0.21), residues: 599 sheet: -2.11 (0.56), residues: 83 loop : -1.79 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 27 HIS 0.005 0.001 HIS A1042 PHE 0.035 0.002 PHE A 93 TYR 0.014 0.002 TYR A1037 ARG 0.004 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 169 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.5579 (tt0) cc_final: 0.4542 (tm-30) REVERT: A 78 ARG cc_start: 0.8719 (tpt-90) cc_final: 0.8437 (tpp-160) REVERT: A 277 MET cc_start: 0.7735 (mmt) cc_final: 0.7314 (mmm) REVERT: A 381 TRP cc_start: 0.8262 (OUTLIER) cc_final: 0.7536 (t-100) REVERT: A 415 THR cc_start: 0.7659 (m) cc_final: 0.7459 (t) REVERT: A 550 TYR cc_start: 0.7982 (p90) cc_final: 0.7629 (p90) REVERT: A 584 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8452 (mt-10) REVERT: A 714 ARG cc_start: 0.7450 (ptp90) cc_final: 0.6875 (ptm-80) REVERT: A 751 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7414 (pt) REVERT: A 825 TYR cc_start: 0.8752 (t80) cc_final: 0.7979 (t80) REVERT: A 912 MET cc_start: 0.6913 (mmp) cc_final: 0.6605 (mmt) REVERT: A 1005 ASP cc_start: 0.8840 (t0) cc_final: 0.8507 (t0) REVERT: A 1089 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7313 (tm-30) REVERT: A 1097 ASP cc_start: 0.7613 (t70) cc_final: 0.7279 (t70) REVERT: A 1106 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8041 (mp) REVERT: A 1110 PHE cc_start: 0.8504 (t80) cc_final: 0.8268 (t80) REVERT: A 1127 MET cc_start: 0.8310 (ttp) cc_final: 0.7939 (tpp) REVERT: A 1168 CYS cc_start: 0.6470 (t) cc_final: 0.5885 (t) outliers start: 53 outliers final: 32 residues processed: 199 average time/residue: 0.1731 time to fit residues: 51.4917 Evaluate side-chains 193 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 158 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 381 TRP Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 788 LYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9753 Z= 0.211 Angle : 0.760 11.438 13296 Z= 0.357 Chirality : 0.045 0.235 1557 Planarity : 0.004 0.039 1664 Dihedral : 11.908 108.982 1801 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.26 % Favored : 93.57 % Rotamer: Outliers : 4.62 % Allowed : 20.94 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.60 (0.24), residues: 1167 helix: 0.82 (0.21), residues: 598 sheet: -1.82 (0.49), residues: 101 loop : -1.67 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 27 HIS 0.004 0.001 HIS A1042 PHE 0.030 0.001 PHE A 93 TYR 0.014 0.001 TYR A 44 ARG 0.003 0.000 ARG A1183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 176 time to evaluate : 1.038 Fit side-chains REVERT: A 43 GLU cc_start: 0.5006 (tt0) cc_final: 0.4125 (tm-30) REVERT: A 78 ARG cc_start: 0.8728 (tpt-90) cc_final: 0.8439 (tpp-160) REVERT: A 193 MET cc_start: 0.8934 (mmm) cc_final: 0.8226 (mpp) REVERT: A 277 MET cc_start: 0.7685 (mmt) cc_final: 0.7351 (mmm) REVERT: A 406 GLU cc_start: 0.8675 (mp0) cc_final: 0.8407 (mp0) REVERT: A 506 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.7461 (t80) REVERT: A 550 TYR cc_start: 0.7903 (p90) cc_final: 0.7497 (p90) REVERT: A 584 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8359 (mt-10) REVERT: A 825 TYR cc_start: 0.8760 (t80) cc_final: 0.8070 (t80) REVERT: A 912 MET cc_start: 0.6973 (mmp) cc_final: 0.6742 (mmt) REVERT: A 1013 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6285 (mmmt) REVERT: A 1089 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7308 (tm-30) REVERT: A 1097 ASP cc_start: 0.7551 (t70) cc_final: 0.7190 (t0) REVERT: A 1106 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8054 (mp) REVERT: A 1110 PHE cc_start: 0.8497 (t80) cc_final: 0.8274 (t80) REVERT: A 1127 MET cc_start: 0.8136 (ttp) cc_final: 0.7857 (tpp) REVERT: A 1168 CYS cc_start: 0.6617 (t) cc_final: 0.6041 (t) REVERT: A 1235 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8336 (mt) outliers start: 47 outliers final: 31 residues processed: 201 average time/residue: 0.1696 time to fit residues: 50.9936 Evaluate side-chains 196 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 788 LYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9753 Z= 0.214 Angle : 0.741 11.139 13296 Z= 0.351 Chirality : 0.045 0.242 1557 Planarity : 0.004 0.039 1664 Dihedral : 11.220 109.442 1801 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.34 % Favored : 93.57 % Rotamer: Outliers : 5.31 % Allowed : 21.73 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.42 (0.25), residues: 1167 helix: 0.93 (0.21), residues: 605 sheet: -1.61 (0.50), residues: 101 loop : -1.59 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 27 HIS 0.003 0.001 HIS A 758 PHE 0.024 0.001 PHE A 504 TYR 0.015 0.001 TYR A 44 ARG 0.003 0.000 ARG A1183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 166 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.5120 (tt0) cc_final: 0.4325 (tm-30) REVERT: A 78 ARG cc_start: 0.8734 (tpt-90) cc_final: 0.8436 (tpp-160) REVERT: A 101 PHE cc_start: 0.8215 (t80) cc_final: 0.7971 (m-80) REVERT: A 184 CYS cc_start: 0.2548 (OUTLIER) cc_final: 0.2173 (p) REVERT: A 277 MET cc_start: 0.7846 (mmt) cc_final: 0.7510 (mmm) REVERT: A 506 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7535 (t80) REVERT: A 550 TYR cc_start: 0.7984 (p90) cc_final: 0.7528 (p90) REVERT: A 584 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8322 (mt-10) REVERT: A 825 TYR cc_start: 0.8748 (t80) cc_final: 0.8016 (t80) REVERT: A 912 MET cc_start: 0.7031 (mmp) cc_final: 0.6728 (mmt) REVERT: A 958 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7105 (mtm180) REVERT: A 1005 ASP cc_start: 0.8834 (t0) cc_final: 0.8614 (t0) REVERT: A 1013 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6344 (mmmt) REVERT: A 1069 MET cc_start: 0.8737 (tpp) cc_final: 0.8241 (tpp) REVERT: A 1097 ASP cc_start: 0.7545 (t70) cc_final: 0.7200 (t0) REVERT: A 1106 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8055 (mp) REVERT: A 1110 PHE cc_start: 0.8504 (t80) cc_final: 0.8297 (t80) REVERT: A 1127 MET cc_start: 0.8222 (ttp) cc_final: 0.7917 (tpp) REVERT: A 1168 CYS cc_start: 0.6690 (t) cc_final: 0.6092 (t) outliers start: 54 outliers final: 42 residues processed: 195 average time/residue: 0.1757 time to fit residues: 50.5511 Evaluate side-chains 204 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 157 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 788 LYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 93 optimal weight: 0.0870 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 0.1980 chunk 59 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.8564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1170 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9753 Z= 0.280 Angle : 0.761 11.475 13296 Z= 0.363 Chirality : 0.045 0.242 1557 Planarity : 0.004 0.043 1664 Dihedral : 11.005 107.322 1801 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 5.70 % Allowed : 22.81 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.42 (0.25), residues: 1167 helix: 0.90 (0.21), residues: 603 sheet: -1.51 (0.51), residues: 101 loop : -1.55 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 27 HIS 0.003 0.001 HIS A1042 PHE 0.030 0.002 PHE A 504 TYR 0.021 0.002 TYR A 420 ARG 0.002 0.000 ARG A 835 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 162 time to evaluate : 1.115 Fit side-chains REVERT: A 78 ARG cc_start: 0.8739 (tpt-90) cc_final: 0.8419 (tpp-160) REVERT: A 89 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8256 (mt) REVERT: A 101 PHE cc_start: 0.8342 (t80) cc_final: 0.8029 (m-80) REVERT: A 184 CYS cc_start: 0.2512 (OUTLIER) cc_final: 0.2160 (p) REVERT: A 277 MET cc_start: 0.7731 (mmt) cc_final: 0.7441 (mmm) REVERT: A 550 TYR cc_start: 0.8077 (p90) cc_final: 0.7648 (p90) REVERT: A 584 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8290 (mt-10) REVERT: A 632 PHE cc_start: 0.6982 (t80) cc_final: 0.6762 (t80) REVERT: A 825 TYR cc_start: 0.8757 (t80) cc_final: 0.8048 (t80) REVERT: A 912 MET cc_start: 0.6876 (mmp) cc_final: 0.6617 (mmt) REVERT: A 958 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7226 (mtm180) REVERT: A 1005 ASP cc_start: 0.8835 (t0) cc_final: 0.8583 (t0) REVERT: A 1013 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6498 (mmmt) REVERT: A 1097 ASP cc_start: 0.7453 (t70) cc_final: 0.7121 (t0) REVERT: A 1106 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8060 (mp) REVERT: A 1110 PHE cc_start: 0.8543 (t80) cc_final: 0.8339 (t80) REVERT: A 1127 MET cc_start: 0.8320 (ttp) cc_final: 0.7949 (tpp) REVERT: A 1168 CYS cc_start: 0.6737 (t) cc_final: 0.6122 (t) REVERT: A 1202 ILE cc_start: 0.8697 (mp) cc_final: 0.8431 (mt) outliers start: 58 outliers final: 46 residues processed: 198 average time/residue: 0.1776 time to fit residues: 52.3083 Evaluate side-chains 207 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 156 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 95 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 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 0.058 9753 Z= 0.200 Angle : 0.726 11.329 13296 Z= 0.344 Chirality : 0.044 0.230 1557 Planarity : 0.004 0.044 1664 Dihedral : 10.497 102.801 1801 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.62 % Allowed : 23.80 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.25), residues: 1167 helix: 1.00 (0.21), residues: 603 sheet: -1.34 (0.53), residues: 101 loop : -1.49 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 27 HIS 0.003 0.001 HIS A 758 PHE 0.032 0.001 PHE A 504 TYR 0.022 0.001 TYR A 420 ARG 0.002 0.000 ARG A1183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 162 time to evaluate : 1.079 Fit side-chains REVERT: A 78 ARG cc_start: 0.8735 (tpt-90) cc_final: 0.8428 (tpp-160) REVERT: A 89 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8170 (mt) REVERT: A 101 PHE cc_start: 0.8393 (t80) cc_final: 0.8043 (m-80) REVERT: A 184 CYS cc_start: 0.2330 (OUTLIER) cc_final: 0.1976 (p) REVERT: A 277 MET cc_start: 0.7828 (mmt) cc_final: 0.7513 (mmm) REVERT: A 550 TYR cc_start: 0.8035 (p90) cc_final: 0.7611 (p90) REVERT: A 578 GLN cc_start: 0.8277 (mp-120) cc_final: 0.7982 (mp10) REVERT: A 584 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8411 (mt-10) REVERT: A 825 TYR cc_start: 0.8777 (t80) cc_final: 0.8111 (t80) REVERT: A 958 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7085 (mtm180) REVERT: A 1013 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6488 (mmmt) REVERT: A 1097 ASP cc_start: 0.7428 (t70) cc_final: 0.7120 (t0) REVERT: A 1106 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8099 (mp) REVERT: A 1127 MET cc_start: 0.8210 (ttp) cc_final: 0.7919 (tpp) REVERT: A 1168 CYS cc_start: 0.6886 (t) cc_final: 0.6198 (t) REVERT: A 1202 ILE cc_start: 0.8744 (mp) cc_final: 0.8479 (mt) REVERT: A 1235 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8314 (mt) outliers start: 47 outliers final: 40 residues processed: 193 average time/residue: 0.1742 time to fit residues: 50.4020 Evaluate side-chains 199 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 153 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 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 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9753 Z= 0.238 Angle : 0.728 10.765 13296 Z= 0.348 Chirality : 0.044 0.230 1557 Planarity : 0.004 0.047 1664 Dihedral : 10.176 94.714 1801 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 5.31 % Allowed : 24.19 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.25), residues: 1167 helix: 1.01 (0.21), residues: 604 sheet: -1.30 (0.53), residues: 101 loop : -1.41 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 27 HIS 0.002 0.001 HIS A 758 PHE 0.035 0.002 PHE A 504 TYR 0.015 0.001 TYR A 709 ARG 0.002 0.000 ARG A 835 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 154 time to evaluate : 1.092 Fit side-chains REVERT: A 78 ARG cc_start: 0.8728 (tpt-90) cc_final: 0.8425 (tpp-160) REVERT: A 89 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8187 (mt) REVERT: A 101 PHE cc_start: 0.8380 (t80) cc_final: 0.8056 (m-80) REVERT: A 184 CYS cc_start: 0.2614 (OUTLIER) cc_final: 0.2252 (p) REVERT: A 277 MET cc_start: 0.7800 (mmt) cc_final: 0.7506 (mmm) REVERT: A 550 TYR cc_start: 0.8087 (p90) cc_final: 0.7680 (p90) REVERT: A 578 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: A 584 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8305 (mt-10) REVERT: A 819 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6640 (tpt-90) REVERT: A 825 TYR cc_start: 0.8803 (t80) cc_final: 0.8102 (t80) REVERT: A 958 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7138 (mtm180) REVERT: A 1013 LYS cc_start: 0.7270 (OUTLIER) cc_final: 0.6684 (mmmt) REVERT: A 1069 MET cc_start: 0.8804 (tpp) cc_final: 0.8336 (tpp) REVERT: A 1097 ASP cc_start: 0.7387 (t70) cc_final: 0.7065 (t0) REVERT: A 1106 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8072 (mp) REVERT: A 1127 MET cc_start: 0.8233 (ttp) cc_final: 0.7933 (tpp) REVERT: A 1168 CYS cc_start: 0.6912 (t) cc_final: 0.6272 (t) REVERT: A 1202 ILE cc_start: 0.8764 (mp) cc_final: 0.8544 (mt) REVERT: A 1235 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8325 (mt) outliers start: 54 outliers final: 42 residues processed: 188 average time/residue: 0.1744 time to fit residues: 49.0467 Evaluate side-chains 202 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 152 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 578 GLN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9753 Z= 0.190 Angle : 0.731 15.352 13296 Z= 0.346 Chirality : 0.044 0.228 1557 Planarity : 0.004 0.045 1664 Dihedral : 9.731 83.015 1800 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.92 % Allowed : 24.58 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.25), residues: 1167 helix: 1.17 (0.21), residues: 598 sheet: -1.20 (0.54), residues: 101 loop : -1.44 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 27 HIS 0.003 0.000 HIS A 758 PHE 0.036 0.001 PHE A 504 TYR 0.026 0.001 TYR A 420 ARG 0.002 0.000 ARG A1183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 164 time to evaluate : 1.083 Fit side-chains REVERT: A 78 ARG cc_start: 0.8729 (tpt-90) cc_final: 0.8430 (tpp-160) REVERT: A 89 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8255 (mt) REVERT: A 101 PHE cc_start: 0.8352 (t80) cc_final: 0.8132 (m-80) REVERT: A 184 CYS cc_start: 0.2752 (OUTLIER) cc_final: 0.2371 (p) REVERT: A 277 MET cc_start: 0.7876 (mmt) cc_final: 0.7557 (mmm) REVERT: A 550 TYR cc_start: 0.8068 (p90) cc_final: 0.7683 (p90) REVERT: A 578 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8061 (mp10) REVERT: A 584 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8332 (mt-10) REVERT: A 688 GLU cc_start: 0.7564 (mp0) cc_final: 0.7295 (mp0) REVERT: A 819 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6848 (tpt-90) REVERT: A 825 TYR cc_start: 0.8811 (t80) cc_final: 0.8090 (t80) REVERT: A 958 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7138 (mtm180) REVERT: A 1097 ASP cc_start: 0.7319 (t70) cc_final: 0.7031 (t0) REVERT: A 1127 MET cc_start: 0.8169 (ttp) cc_final: 0.7924 (tpp) REVERT: A 1168 CYS cc_start: 0.6913 (t) cc_final: 0.6282 (t) REVERT: A 1235 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8370 (mt) outliers start: 50 outliers final: 39 residues processed: 193 average time/residue: 0.1809 time to fit residues: 51.7016 Evaluate side-chains 200 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 155 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 92 GLN Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 578 GLN Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9753 Z= 0.232 Angle : 0.746 13.743 13296 Z= 0.356 Chirality : 0.044 0.217 1557 Planarity : 0.004 0.047 1664 Dihedral : 9.304 81.596 1796 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.11 % Favored : 92.80 % Rotamer: Outliers : 4.33 % Allowed : 25.47 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.25), residues: 1167 helix: 1.16 (0.21), residues: 593 sheet: -1.15 (0.54), residues: 101 loop : -1.38 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 27 HIS 0.002 0.001 HIS A 758 PHE 0.042 0.002 PHE A 503 TYR 0.017 0.001 TYR A 709 ARG 0.001 0.000 ARG A 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 152 time to evaluate : 0.969 Fit side-chains REVERT: A 78 ARG cc_start: 0.8730 (tpt-90) cc_final: 0.8429 (tpp-160) REVERT: A 89 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8287 (mt) REVERT: A 101 PHE cc_start: 0.8405 (t80) cc_final: 0.8133 (m-80) REVERT: A 184 CYS cc_start: 0.2847 (OUTLIER) cc_final: 0.2474 (p) REVERT: A 277 MET cc_start: 0.8186 (mmt) cc_final: 0.7942 (mmm) REVERT: A 406 GLU cc_start: 0.8646 (mp0) cc_final: 0.8440 (mp0) REVERT: A 550 TYR cc_start: 0.8134 (p90) cc_final: 0.7785 (p90) REVERT: A 584 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8371 (mt-10) REVERT: A 688 GLU cc_start: 0.7669 (mp0) cc_final: 0.7338 (mp0) REVERT: A 819 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7026 (tpt-90) REVERT: A 825 TYR cc_start: 0.8814 (t80) cc_final: 0.8140 (t80) REVERT: A 958 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7154 (mtm180) REVERT: A 1097 ASP cc_start: 0.7323 (t70) cc_final: 0.7030 (t0) REVERT: A 1127 MET cc_start: 0.8202 (ttp) cc_final: 0.7943 (tpp) REVERT: A 1168 CYS cc_start: 0.6945 (t) cc_final: 0.6339 (t) REVERT: A 1235 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8351 (mt) outliers start: 44 outliers final: 37 residues processed: 177 average time/residue: 0.1779 time to fit residues: 46.7522 Evaluate side-chains 193 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 184 CYS Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 575 GLU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 778 CYS Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 819 ARG Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 958 ARG Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1159 MET Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1205 THR Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.143605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113154 restraints weight = 16668.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112704 restraints weight = 9693.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.113909 restraints weight = 7966.563| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9753 Z= 0.190 Angle : 0.723 14.032 13296 Z= 0.344 Chirality : 0.044 0.228 1557 Planarity : 0.004 0.048 1664 Dihedral : 8.831 79.413 1793 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.51 % Favored : 93.40 % Rotamer: Outliers : 3.93 % Allowed : 25.57 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.25), residues: 1167 helix: 1.20 (0.22), residues: 599 sheet: -1.09 (0.53), residues: 101 loop : -1.38 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 27 HIS 0.003 0.001 HIS A 758 PHE 0.033 0.001 PHE A 504 TYR 0.028 0.001 TYR A 420 ARG 0.002 0.000 ARG A1183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2111.59 seconds wall clock time: 39 minutes 9.37 seconds (2349.37 seconds total)