Starting phenix.real_space_refine on Fri Feb 16 18:28:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5u_21548/02_2024/6w5u_21548_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5u_21548/02_2024/6w5u_21548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5u_21548/02_2024/6w5u_21548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5u_21548/02_2024/6w5u_21548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5u_21548/02_2024/6w5u_21548_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5u_21548/02_2024/6w5u_21548_updated.pdb" } resolution = 3.9 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 70 5.16 5 C 6128 2.51 5 N 1495 2.21 5 O 1781 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 127": "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 606": "OE1" <-> "OE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A GLU 713": "OE1" <-> "OE2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A GLU 718": "OE1" <-> "OE2" Residue "A GLU 742": "OE1" <-> "OE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A ARG 934": "NH1" <-> "NH2" Residue "A ARG 978": "NH1" <-> "NH2" Residue "A ARG 980": "NH1" <-> "NH2" Residue "A ARG 989": "NH1" <-> "NH2" Residue "A GLU 1067": "OE1" <-> "OE2" Residue "A GLU 1120": "OE1" <-> "OE2" Residue "A GLU 1166": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9474 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9158 Classifications: {'peptide': 1175} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1111} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 33 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: {'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: "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: 5.74, per 1000 atoms: 0.61 Number of scatterers: 9474 At special positions: 0 Unit cell: (103.602, 91.348, 145.934, 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 70 16.00 O 1781 8.00 N 1495 7.00 C 6128 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=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.03 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=1.45 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=1.99 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.02 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.02 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.02 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM 9237 O5 NAG D 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9237 O5 NAG D 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG C 2 " - " BMA 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: 4.70 Conformation dependent library (CDL) restraints added in 1.7 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: 47 helices and 5 sheets defined 52.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 56 through 66 Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 187 through 194 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 293 removed outlier: 4.246A pdb=" N ALA A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 348 removed outlier: 3.944A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 370 removed outlier: 4.734A pdb=" N GLY A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LEU A 368 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 5.517A 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 removed outlier: 3.605A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS A 398 " --> pdb=" O TYR A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 437 through 452 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 Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' 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: 3.600A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 617 Processing helix chain 'A' and resid 621 through 638 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 Processing helix chain 'A' and resid 825 through 829 Processing helix chain 'A' and resid 832 through 851 Proline residue: A 836 - end of helix 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 943 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 1003 Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1016 through 1019 No H-bonds generated for 'chain 'A' and resid 1016 through 1019' Processing helix chain 'A' and resid 1048 through 1069 Processing helix chain 'A' and resid 1083 through 1085 No H-bonds generated for 'chain 'A' and resid 1083 through 1085' 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: 3.907A pdb=" N GLY A1162 " --> pdb=" O VAL A1158 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL A1165 " --> pdb=" O CYS A1161 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A1167 " --> pdb=" O ILE A1163 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A1172 " --> pdb=" O CYS A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1213 removed outlier: 4.397A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A1200 " --> pdb=" O SER A1196 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU A1204 " --> pdb=" O SER A1200 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A1205 " --> pdb=" O GLY A1201 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A1212 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A1213 " --> pdb=" O GLY A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1251 removed outlier: 4.655A pdb=" N PHE A1226 " --> pdb=" O GLN A1222 " (cutoff:3.500A) Proline residue: A1245 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 127 through 129 Processing sheet with id= B, first strand: chain 'A' and resid 205 through 210 removed outlier: 6.573A pdb=" N LEU A 144 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL A 208 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR A 146 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER A 210 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL A 148 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLN A 145 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL A 123 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TYR A 147 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU A 121 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 409 through 411 Processing sheet with id= D, first strand: chain 'A' and resid 418 through 420 Processing sheet with id= E, first strand: chain 'A' and resid 1039 through 1041 409 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2877 1.34 - 1.46: 2333 1.46 - 1.58: 4407 1.58 - 1.71: 1 1.71 - 1.83: 99 Bond restraints: 9717 Sorted by residual: bond pdb=" C ALA A 165 " pdb=" N PRO A 166 " ideal model delta sigma weight residual 1.330 1.465 -0.135 1.25e-02 6.40e+03 1.17e+02 bond pdb=" C TYR A 56 " pdb=" N ASP A 57 " ideal model delta sigma weight residual 1.334 1.258 0.077 1.27e-02 6.20e+03 3.65e+01 bond pdb=" C PHE A 565 " pdb=" N PRO A 566 " ideal model delta sigma weight residual 1.332 1.259 0.072 1.30e-02 5.92e+03 3.11e+01 bond pdb=" C TYR A 102 " pdb=" N ASN A 103 " ideal model delta sigma weight residual 1.335 1.408 -0.074 1.36e-02 5.41e+03 2.93e+01 bond pdb=" C ASP A 170 " pdb=" N LYS A 171 " ideal model delta sigma weight residual 1.332 1.396 -0.064 1.40e-02 5.10e+03 2.09e+01 ... (remaining 9712 not shown) Histogram of bond angle deviations from ideal: 84.63 - 98.22: 1 98.22 - 111.81: 4792 111.81 - 125.39: 8295 125.39 - 138.98: 157 138.98 - 152.57: 2 Bond angle restraints: 13247 Sorted by residual: angle pdb=" N LYS A 171 " pdb=" CA LYS A 171 " pdb=" CB LYS A 171 " ideal model delta sigma weight residual 110.49 152.57 -42.08 1.69e+00 3.50e-01 6.20e+02 angle pdb=" C ALA A 165 " pdb=" N PRO A 166 " pdb=" CA PRO A 166 " ideal model delta sigma weight residual 120.21 107.42 12.79 9.60e-01 1.09e+00 1.78e+02 angle pdb=" N LYS A 171 " pdb=" CA LYS A 171 " pdb=" C LYS A 171 " ideal model delta sigma weight residual 110.80 84.63 26.17 2.13e+00 2.20e-01 1.51e+02 angle pdb=" N VAL A 26 " pdb=" CA VAL A 26 " pdb=" C VAL A 26 " ideal model delta sigma weight residual 113.53 104.89 8.64 9.80e-01 1.04e+00 7.77e+01 angle pdb=" N GLN A 88 " pdb=" CA GLN A 88 " pdb=" C GLN A 88 " ideal model delta sigma weight residual 111.07 119.98 -8.91 1.07e+00 8.73e-01 6.94e+01 ... (remaining 13242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.60: 5550 24.60 - 49.20: 376 49.20 - 73.79: 103 73.79 - 98.39: 24 98.39 - 122.99: 35 Dihedral angle restraints: 6088 sinusoidal: 2667 harmonic: 3421 Sorted by residual: dihedral pdb=" C ASP A 170 " pdb=" N ASP A 170 " pdb=" CA ASP A 170 " pdb=" CB ASP A 170 " ideal model delta harmonic sigma weight residual -122.60 -167.11 44.51 0 2.50e+00 1.60e-01 3.17e+02 dihedral pdb=" N ASP A 170 " pdb=" C ASP A 170 " pdb=" CA ASP A 170 " pdb=" CB ASP A 170 " ideal model delta harmonic sigma weight residual 122.80 165.01 -42.21 0 2.50e+00 1.60e-01 2.85e+02 dihedral pdb=" N LYS A 171 " pdb=" C LYS A 171 " pdb=" CA LYS A 171 " pdb=" CB LYS A 171 " ideal model delta harmonic sigma weight residual 122.80 156.62 -33.82 0 2.50e+00 1.60e-01 1.83e+02 ... (remaining 6085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.950: 1552 0.950 - 1.899: 2 1.899 - 2.849: 1 2.849 - 3.798: 0 3.798 - 4.748: 1 Chirality restraints: 1556 Sorted by residual: 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 2.35 -4.75 2.00e-02 2.50e+03 5.63e+04 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-02 2.50e+03 9.72e+02 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 -1.90 -0.50 2.00e-02 2.50e+03 6.14e+02 ... (remaining 1553 not shown) Planarity restraints: 1673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.308 2.00e-02 2.50e+03 2.60e-01 8.43e+02 pdb=" C7 NAG D 1 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.447 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.301 2.00e-02 2.50e+03 2.53e-01 8.00e+02 pdb=" C7 NAG B 2 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.433 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 524 " -0.128 2.00e-02 2.50e+03 2.34e-01 6.83e+02 pdb=" CG ASN A 524 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 524 " 0.259 2.00e-02 2.50e+03 pdb=" ND2 ASN A 524 " -0.342 2.00e-02 2.50e+03 pdb=" C1 NAG A1405 " 0.265 2.00e-02 2.50e+03 ... (remaining 1670 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 42 2.37 - 3.00: 6679 3.00 - 3.64: 14145 3.64 - 4.27: 21564 4.27 - 4.90: 35220 Nonbonded interactions: 77650 Sorted by model distance: nonbonded pdb=" OD1 ASN A 931 " pdb=" O5 NAG D 1 " model vdw 1.741 3.040 nonbonded pdb=" CG ASN A 931 " pdb=" O5 NAG D 1 " model vdw 1.856 2.616 nonbonded pdb=" O3 NAG A1402 " pdb=" O7 NAG A1402 " model vdw 1.982 2.440 nonbonded pdb=" OD2 ASP A 131 " pdb=" N THR A 134 " model vdw 2.035 2.520 nonbonded pdb=" N GLY A1181 " pdb=" OE2 GLU A1185 " model vdw 2.053 2.520 ... (remaining 77645 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' selection = chain 'D' } 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 3.460 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 29.630 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.011 0.135 9717 Z= 0.732 Angle : 1.525 42.080 13247 Z= 0.871 Chirality : 0.157 4.748 1556 Planarity : 0.012 0.260 1660 Dihedral : 20.438 122.991 3843 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 63.51 Ramachandran Plot: Outliers : 1.03 % Allowed : 8.48 % Favored : 90.49 % Rotamer: Outliers : 6.82 % Allowed : 10.19 % Favored : 82.99 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 3.23 % 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: -2.76 (0.23), residues: 1167 helix: -0.93 (0.20), residues: 601 sheet: -2.10 (0.60), residues: 86 loop : -2.94 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.005 TRP A1145 HIS 0.010 0.003 HIS A1239 PHE 0.040 0.004 PHE A 339 TYR 0.030 0.003 TYR A 423 ARG 0.007 0.001 ARG A 389 *********************** 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 298 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 229 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8693 (m-40) cc_final: 0.8463 (m-40) REVERT: A 110 GLU cc_start: 0.8136 (tp30) cc_final: 0.7926 (tt0) REVERT: A 145 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.6759 (mm110) REVERT: A 206 THR cc_start: 0.6262 (OUTLIER) cc_final: 0.6058 (p) REVERT: A 612 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8250 (tp30) REVERT: A 633 LEU cc_start: 0.9361 (tp) cc_final: 0.9134 (tt) REVERT: A 707 GLN cc_start: 0.8571 (mm110) cc_final: 0.8367 (mm110) REVERT: A 712 ASP cc_start: 0.8020 (t70) cc_final: 0.7672 (t0) REVERT: A 714 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7590 (pmt170) REVERT: A 754 MET cc_start: 0.7675 (tmm) cc_final: 0.7219 (ttp) REVERT: A 766 LEU cc_start: 0.8664 (tp) cc_final: 0.8397 (tp) REVERT: A 858 ILE cc_start: 0.9394 (mm) cc_final: 0.8589 (tt) REVERT: A 1114 MET cc_start: 0.8323 (tmm) cc_final: 0.7744 (tmm) REVERT: A 1143 TRP cc_start: 0.7858 (t60) cc_final: 0.7506 (t60) REVERT: A 1175 PHE cc_start: 0.8426 (t80) cc_final: 0.7919 (t80) REVERT: A 1222 GLN cc_start: 0.7866 (tt0) cc_final: 0.7388 (tm-30) outliers start: 69 outliers final: 23 residues processed: 276 average time/residue: 0.2092 time to fit residues: 80.3407 Evaluate side-chains 188 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 612 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 855 LYS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1116 LEU 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: 10.0000 chunk 49 optimal weight: 0.0770 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 122 ASN A 145 GLN A 215 HIS A 349 ASN A 489 GLN A 497 HIS A 530 HIS ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A 775 GLN A 793 ASN A 884 HIS A1016 HIS ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9717 Z= 0.240 Angle : 0.920 12.892 13247 Z= 0.432 Chirality : 0.056 0.492 1556 Planarity : 0.005 0.057 1660 Dihedral : 18.264 118.374 1846 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.26 % Favored : 93.49 % Rotamer: Outliers : 4.65 % Allowed : 15.33 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.31 (0.24), residues: 1167 helix: 0.03 (0.21), residues: 604 sheet: -1.41 (0.58), residues: 79 loop : -1.90 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 27 HIS 0.005 0.002 HIS A1016 PHE 0.023 0.002 PHE A 998 TYR 0.034 0.002 TYR A 515 ARG 0.009 0.001 ARG A 978 *********************** 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 251 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 204 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8463 (mtm110) cc_final: 0.8204 (ttp-110) REVERT: A 103 ASN cc_start: 0.8881 (m-40) cc_final: 0.8577 (m-40) REVERT: A 107 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8829 (tp) REVERT: A 110 GLU cc_start: 0.8485 (tp30) cc_final: 0.8135 (tp30) REVERT: A 460 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7261 (mm-30) REVERT: A 714 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7285 (ptt-90) REVERT: A 742 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6505 (mt-10) REVERT: A 766 LEU cc_start: 0.8509 (tp) cc_final: 0.8005 (tp) REVERT: A 857 ASP cc_start: 0.7531 (m-30) cc_final: 0.7328 (m-30) REVERT: A 858 ILE cc_start: 0.9182 (mm) cc_final: 0.8523 (tt) REVERT: A 982 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8267 (tm) REVERT: A 1106 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8450 (mp) REVERT: A 1114 MET cc_start: 0.8236 (tmm) cc_final: 0.7676 (tmm) REVERT: A 1143 TRP cc_start: 0.7884 (t60) cc_final: 0.7405 (t60) REVERT: A 1175 PHE cc_start: 0.8074 (t80) cc_final: 0.7673 (t80) REVERT: A 1185 GLU cc_start: 0.7839 (pt0) cc_final: 0.7597 (mp0) REVERT: A 1220 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8939 (tt) REVERT: A 1221 PHE cc_start: 0.8288 (m-10) cc_final: 0.8034 (m-10) outliers start: 47 outliers final: 24 residues processed: 235 average time/residue: 0.2076 time to fit residues: 69.2382 Evaluate side-chains 186 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 914 CYS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1048 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1161 CYS Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 6.9990 chunk 32 optimal weight: 0.0050 chunk 88 optimal weight: 0.0370 chunk 72 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 overall best weight: 0.4272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN A 407 GLN A 447 GLN A 884 HIS A1008 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9717 Z= 0.193 Angle : 0.789 10.013 13247 Z= 0.371 Chirality : 0.051 0.586 1556 Planarity : 0.005 0.047 1660 Dihedral : 15.941 105.268 1811 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.91 % Favored : 93.83 % Rotamer: Outliers : 3.46 % Allowed : 18.69 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.64 (0.25), residues: 1167 helix: 0.67 (0.21), residues: 588 sheet: -1.18 (0.52), residues: 90 loop : -1.61 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 27 HIS 0.011 0.001 HIS A 497 PHE 0.017 0.001 PHE A 488 TYR 0.025 0.002 TYR A 515 ARG 0.004 0.001 ARG A 389 *********************** 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 213 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 178 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8586 (mtm110) cc_final: 0.8328 (ttp-110) REVERT: A 103 ASN cc_start: 0.8795 (m-40) cc_final: 0.8457 (m-40) REVERT: A 217 MET cc_start: 0.2177 (mmt) cc_final: 0.1901 (mmt) REVERT: A 376 ASN cc_start: 0.8302 (t0) cc_final: 0.8094 (t0) REVERT: A 393 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7481 (tm-30) REVERT: A 488 PHE cc_start: 0.8888 (m-80) cc_final: 0.8660 (m-10) REVERT: A 697 VAL cc_start: 0.7654 (m) cc_final: 0.7445 (t) REVERT: A 714 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7051 (ptt-90) REVERT: A 742 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6447 (mt-10) REVERT: A 766 LEU cc_start: 0.8439 (tp) cc_final: 0.7982 (tp) REVERT: A 857 ASP cc_start: 0.7554 (m-30) cc_final: 0.7252 (m-30) REVERT: A 858 ILE cc_start: 0.9204 (mm) cc_final: 0.8539 (tt) REVERT: A 909 CYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8302 (p) REVERT: A 982 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8315 (tm) REVERT: A 991 GLN cc_start: 0.8582 (pt0) cc_final: 0.8312 (pt0) REVERT: A 1106 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8507 (mp) REVERT: A 1114 MET cc_start: 0.8138 (tmm) cc_final: 0.7558 (tmm) REVERT: A 1143 TRP cc_start: 0.7851 (t60) cc_final: 0.7375 (t60) REVERT: A 1175 PHE cc_start: 0.8068 (t80) cc_final: 0.7812 (t80) outliers start: 35 outliers final: 24 residues processed: 203 average time/residue: 0.1991 time to fit residues: 58.2862 Evaluate side-chains 186 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1122 TRP Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1218 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.9990 chunk 80 optimal weight: 0.0970 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9717 Z= 0.243 Angle : 0.785 10.937 13247 Z= 0.367 Chirality : 0.051 0.603 1556 Planarity : 0.004 0.039 1660 Dihedral : 14.557 104.047 1807 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.51 % Favored : 93.40 % Rotamer: Outliers : 4.65 % Allowed : 19.09 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.25), residues: 1167 helix: 0.78 (0.21), residues: 588 sheet: -1.08 (0.54), residues: 91 loop : -1.53 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 27 HIS 0.009 0.001 HIS A 497 PHE 0.029 0.002 PHE A 504 TYR 0.018 0.001 TYR A 40 ARG 0.002 0.001 ARG A 978 *********************** 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 211 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 164 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8795 (m-40) cc_final: 0.8437 (m-40) REVERT: A 111 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8597 (tp) REVERT: A 393 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 488 PHE cc_start: 0.9002 (m-80) cc_final: 0.8753 (m-10) REVERT: A 742 GLU cc_start: 0.6727 (mt-10) cc_final: 0.6319 (mt-10) REVERT: A 766 LEU cc_start: 0.8586 (tp) cc_final: 0.8097 (tp) REVERT: A 857 ASP cc_start: 0.7657 (m-30) cc_final: 0.7409 (m-30) REVERT: A 858 ILE cc_start: 0.9334 (mm) cc_final: 0.8748 (tt) REVERT: A 909 CYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8183 (p) REVERT: A 1026 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7807 (pp) REVERT: A 1106 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8492 (mp) REVERT: A 1114 MET cc_start: 0.8081 (tmm) cc_final: 0.7485 (tmm) REVERT: A 1143 TRP cc_start: 0.7891 (t60) cc_final: 0.7424 (t60) REVERT: A 1175 PHE cc_start: 0.8180 (t80) cc_final: 0.7839 (t80) REVERT: A 1193 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.7052 (t-90) outliers start: 47 outliers final: 33 residues processed: 199 average time/residue: 0.1944 time to fit residues: 55.6477 Evaluate side-chains 191 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1122 TRP Chi-restraints excluded: chain A residue 1193 HIS Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1223 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 78 optimal weight: 0.0770 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN A1006 ASN A1193 HIS ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9717 Z= 0.191 Angle : 0.750 10.984 13247 Z= 0.349 Chirality : 0.049 0.545 1556 Planarity : 0.004 0.053 1660 Dihedral : 13.227 102.965 1801 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.91 % Favored : 94.00 % Rotamer: Outliers : 4.65 % Allowed : 20.18 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.25), residues: 1167 helix: 0.94 (0.21), residues: 585 sheet: -0.91 (0.55), residues: 89 loop : -1.48 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 27 HIS 0.009 0.001 HIS A 497 PHE 0.034 0.001 PHE A 504 TYR 0.018 0.001 TYR A 40 ARG 0.005 0.000 ARG A 714 *********************** 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 216 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 169 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8464 (mtm110) cc_final: 0.8246 (ttp-110) REVERT: A 103 ASN cc_start: 0.8749 (m-40) cc_final: 0.8453 (m-40) REVERT: A 111 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8548 (tp) REVERT: A 156 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6345 (tmm) REVERT: A 217 MET cc_start: 0.1961 (mmt) cc_final: 0.1632 (mmt) REVERT: A 393 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7580 (tm-30) REVERT: A 742 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6303 (mt-10) REVERT: A 766 LEU cc_start: 0.8558 (tp) cc_final: 0.8205 (tp) REVERT: A 857 ASP cc_start: 0.7587 (m-30) cc_final: 0.7283 (m-30) REVERT: A 858 ILE cc_start: 0.9309 (mm) cc_final: 0.8731 (tt) REVERT: A 909 CYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8484 (p) REVERT: A 991 GLN cc_start: 0.8611 (pt0) cc_final: 0.8390 (pt0) REVERT: A 1106 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8542 (mp) REVERT: A 1114 MET cc_start: 0.8041 (tmm) cc_final: 0.7406 (tmm) REVERT: A 1143 TRP cc_start: 0.7925 (t60) cc_final: 0.7368 (t60) REVERT: A 1175 PHE cc_start: 0.8048 (t80) cc_final: 0.7684 (t80) outliers start: 47 outliers final: 35 residues processed: 203 average time/residue: 0.1974 time to fit residues: 57.9967 Evaluate side-chains 197 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 158 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1122 TRP Chi-restraints excluded: chain A residue 1150 ASN Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1193 HIS Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1223 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 113 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 ASN A1008 ASN ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 9717 Z= 0.406 Angle : 0.845 10.795 13247 Z= 0.403 Chirality : 0.053 0.567 1556 Planarity : 0.005 0.038 1660 Dihedral : 12.897 107.040 1801 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.03 % Favored : 92.89 % Rotamer: Outliers : 5.64 % Allowed : 20.97 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.58 (0.25), residues: 1167 helix: 0.70 (0.21), residues: 584 sheet: -1.04 (0.55), residues: 89 loop : -1.58 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 27 HIS 0.019 0.002 HIS A1193 PHE 0.020 0.002 PHE A1167 TYR 0.021 0.002 TYR A 423 ARG 0.004 0.001 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 209 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 152 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8749 (m-40) cc_final: 0.8546 (m-40) REVERT: A 156 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6385 (tmm) REVERT: A 393 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 488 PHE cc_start: 0.9091 (m-80) cc_final: 0.8860 (m-10) REVERT: A 742 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6253 (mt-10) REVERT: A 766 LEU cc_start: 0.8782 (tp) cc_final: 0.8292 (tp) REVERT: A 857 ASP cc_start: 0.7850 (m-30) cc_final: 0.7531 (m-30) REVERT: A 858 ILE cc_start: 0.9436 (mm) cc_final: 0.8880 (tt) REVERT: A 909 CYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8084 (p) REVERT: A 1114 MET cc_start: 0.7994 (tmm) cc_final: 0.7341 (tmm) REVERT: A 1143 TRP cc_start: 0.7965 (t60) cc_final: 0.7418 (t60) REVERT: A 1175 PHE cc_start: 0.8128 (t80) cc_final: 0.7750 (t80) outliers start: 57 outliers final: 43 residues processed: 197 average time/residue: 0.2003 time to fit residues: 57.5507 Evaluate side-chains 190 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 145 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1122 TRP Chi-restraints excluded: chain A residue 1150 ASN Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1223 ILE 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: 0.9990 chunk 82 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 45 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 ASN ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9717 Z= 0.183 Angle : 0.752 11.384 13247 Z= 0.351 Chirality : 0.048 0.526 1556 Planarity : 0.004 0.038 1660 Dihedral : 12.146 103.460 1801 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.34 % Favored : 93.57 % Rotamer: Outliers : 4.35 % Allowed : 22.85 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.28 (0.25), residues: 1167 helix: 0.94 (0.21), residues: 584 sheet: -0.91 (0.56), residues: 90 loop : -1.41 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 27 HIS 0.011 0.001 HIS A 497 PHE 0.023 0.001 PHE A1167 TYR 0.020 0.001 TYR A 515 ARG 0.003 0.000 ARG A 714 *********************** 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: 44 poor density : 165 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8413 (mtm110) cc_final: 0.8106 (ttp-110) REVERT: A 103 ASN cc_start: 0.8728 (m-40) cc_final: 0.8412 (m-40) REVERT: A 111 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8538 (tp) REVERT: A 156 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6322 (tmm) REVERT: A 217 MET cc_start: 0.0877 (mmt) cc_final: 0.0194 (mmt) REVERT: A 393 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 460 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: A 742 GLU cc_start: 0.6739 (mt-10) cc_final: 0.6509 (mt-10) REVERT: A 766 LEU cc_start: 0.8659 (tp) cc_final: 0.8301 (tp) REVERT: A 857 ASP cc_start: 0.7659 (m-30) cc_final: 0.7302 (m-30) REVERT: A 858 ILE cc_start: 0.9336 (mm) cc_final: 0.8738 (tt) REVERT: A 909 CYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8231 (p) REVERT: A 1093 THR cc_start: 0.8695 (p) cc_final: 0.8437 (p) REVERT: A 1114 MET cc_start: 0.7985 (tmm) cc_final: 0.7320 (tmm) REVERT: A 1143 TRP cc_start: 0.7860 (t60) cc_final: 0.7336 (t60) REVERT: A 1175 PHE cc_start: 0.8086 (t80) cc_final: 0.7735 (t80) outliers start: 44 outliers final: 34 residues processed: 196 average time/residue: 0.1917 time to fit residues: 54.0629 Evaluate side-chains 193 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 155 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1122 TRP Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1223 ILE Chi-restraints excluded: chain A residue 1228 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9717 Z= 0.223 Angle : 0.781 11.679 13247 Z= 0.366 Chirality : 0.065 1.671 1556 Planarity : 0.004 0.047 1660 Dihedral : 11.964 104.902 1801 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 4.85 % Allowed : 22.16 % Favored : 73.00 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.23 % 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: -0.32 (0.25), residues: 1167 helix: 0.89 (0.21), residues: 597 sheet: -0.84 (0.58), residues: 90 loop : -1.50 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 27 HIS 0.010 0.001 HIS A 497 PHE 0.034 0.001 PHE A1167 TYR 0.025 0.002 TYR A 457 ARG 0.004 0.001 ARG A 96 *********************** 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 210 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 161 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8790 (m-40) cc_final: 0.8475 (m-40) REVERT: A 156 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6344 (tmm) REVERT: A 393 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7671 (tm-30) REVERT: A 703 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7867 (t80) REVERT: A 742 GLU cc_start: 0.6614 (mt-10) cc_final: 0.6361 (mt-10) REVERT: A 766 LEU cc_start: 0.8698 (tp) cc_final: 0.8333 (tp) REVERT: A 857 ASP cc_start: 0.7685 (m-30) cc_final: 0.7361 (m-30) REVERT: A 858 ILE cc_start: 0.9377 (mm) cc_final: 0.8750 (tt) REVERT: A 909 CYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8450 (p) REVERT: A 1093 THR cc_start: 0.8622 (p) cc_final: 0.8396 (p) REVERT: A 1114 MET cc_start: 0.7983 (tmm) cc_final: 0.7259 (tmm) REVERT: A 1143 TRP cc_start: 0.7853 (t60) cc_final: 0.7318 (t60) REVERT: A 1175 PHE cc_start: 0.8120 (t80) cc_final: 0.7803 (t80) outliers start: 49 outliers final: 40 residues processed: 194 average time/residue: 0.2019 time to fit residues: 55.9797 Evaluate side-chains 195 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 152 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1122 TRP Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1207 PHE Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1223 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 ASN ** A1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9717 Z= 0.189 Angle : 0.766 12.321 13247 Z= 0.357 Chirality : 0.054 0.997 1556 Planarity : 0.004 0.042 1660 Dihedral : 11.457 103.950 1798 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.51 % Favored : 93.40 % Rotamer: Outliers : 4.06 % Allowed : 23.44 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1167 helix: 1.00 (0.21), residues: 593 sheet: -0.83 (0.57), residues: 90 loop : -1.42 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 189 HIS 0.010 0.001 HIS A 497 PHE 0.033 0.001 PHE A1110 TYR 0.019 0.001 TYR A 56 ARG 0.009 0.001 ARG A 978 *********************** 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 202 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8746 (m-40) cc_final: 0.8447 (m-40) REVERT: A 111 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8384 (tp) REVERT: A 156 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6235 (tmm) REVERT: A 393 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 457 TYR cc_start: 0.6317 (OUTLIER) cc_final: 0.5932 (p90) REVERT: A 662 LEU cc_start: 0.8259 (mp) cc_final: 0.7969 (mp) REVERT: A 742 GLU cc_start: 0.6511 (mt-10) cc_final: 0.6237 (mt-10) REVERT: A 754 MET cc_start: 0.6859 (ttp) cc_final: 0.6488 (ttt) REVERT: A 766 LEU cc_start: 0.8634 (tp) cc_final: 0.8264 (tp) REVERT: A 857 ASP cc_start: 0.7680 (m-30) cc_final: 0.7404 (m-30) REVERT: A 858 ILE cc_start: 0.9327 (mm) cc_final: 0.8689 (tt) REVERT: A 1114 MET cc_start: 0.7904 (tmm) cc_final: 0.7238 (tmm) REVERT: A 1143 TRP cc_start: 0.7811 (t60) cc_final: 0.7185 (t60) REVERT: A 1167 PHE cc_start: 0.8691 (m-80) cc_final: 0.8477 (m-80) REVERT: A 1175 PHE cc_start: 0.8072 (t80) cc_final: 0.7783 (t80) REVERT: A 1221 PHE cc_start: 0.8465 (m-10) cc_final: 0.8261 (m-80) outliers start: 41 outliers final: 35 residues processed: 190 average time/residue: 0.1962 time to fit residues: 53.4279 Evaluate side-chains 193 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 155 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 457 TYR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1223 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 0.0470 chunk 52 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A1008 ASN ** A1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1193 HIS ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9717 Z= 0.181 Angle : 0.760 12.816 13247 Z= 0.352 Chirality : 0.050 0.589 1556 Planarity : 0.004 0.045 1660 Dihedral : 11.054 104.680 1798 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.43 % Favored : 93.49 % Rotamer: Outliers : 4.06 % Allowed : 23.74 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.17 (0.25), residues: 1167 helix: 1.07 (0.21), residues: 592 sheet: -0.81 (0.57), residues: 90 loop : -1.47 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 189 HIS 0.011 0.001 HIS A 497 PHE 0.030 0.001 PHE A1110 TYR 0.017 0.001 TYR A 40 ARG 0.009 0.000 ARG A 978 ********************** 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 199 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 158 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASN cc_start: 0.8774 (m-40) cc_final: 0.8444 (m-40) REVERT: A 156 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.6092 (tmm) REVERT: A 217 MET cc_start: 0.1408 (tpp) cc_final: 0.0214 (tpp) REVERT: A 393 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7791 (tm-30) REVERT: A 488 PHE cc_start: 0.8866 (m-80) cc_final: 0.8632 (m-10) REVERT: A 595 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7007 (pptt) REVERT: A 662 LEU cc_start: 0.8308 (mp) cc_final: 0.8071 (mp) REVERT: A 742 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6144 (mt-10) REVERT: A 754 MET cc_start: 0.6865 (ttp) cc_final: 0.6520 (ttt) REVERT: A 766 LEU cc_start: 0.8606 (tp) cc_final: 0.8253 (tp) REVERT: A 857 ASP cc_start: 0.7643 (m-30) cc_final: 0.7304 (m-30) REVERT: A 858 ILE cc_start: 0.9315 (mm) cc_final: 0.8661 (tt) REVERT: A 1114 MET cc_start: 0.7778 (tmm) cc_final: 0.7072 (tmm) REVERT: A 1143 TRP cc_start: 0.7775 (t60) cc_final: 0.7225 (t60) REVERT: A 1167 PHE cc_start: 0.8569 (m-80) cc_final: 0.8304 (m-80) REVERT: A 1175 PHE cc_start: 0.8097 (t80) cc_final: 0.7774 (t80) outliers start: 41 outliers final: 36 residues processed: 185 average time/residue: 0.1983 time to fit residues: 53.0761 Evaluate side-chains 188 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 TRP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 607 ARG Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 703 PHE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 757 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 838 VAL Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 973 ASP Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1193 HIS Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1223 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 ASN ** A1137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1239 HIS ** 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 = 0.3836 r_free = 0.3836 target = 0.133804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.104270 restraints weight = 17752.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104068 restraints weight = 10666.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.104813 restraints weight = 9269.346| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9717 Z= 0.233 Angle : 0.769 12.598 13247 Z= 0.360 Chirality : 0.049 0.506 1556 Planarity : 0.004 0.043 1660 Dihedral : 10.947 106.288 1796 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.68 % Favored : 93.23 % Rotamer: Outliers : 3.86 % Allowed : 24.33 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.05 (0.21), residues: 592 sheet: -0.88 (0.56), residues: 90 loop : -1.51 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 189 HIS 0.012 0.002 HIS A1193 PHE 0.027 0.001 PHE A1110 TYR 0.016 0.001 TYR A 40 ARG 0.009 0.001 ARG A 978 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2062.02 seconds wall clock time: 38 minutes 22.42 seconds (2302.42 seconds total)