Starting phenix.real_space_refine on Fri Feb 16 14:15:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzf_24758/02_2024/7rzf_24758.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzf_24758/02_2024/7rzf_24758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzf_24758/02_2024/7rzf_24758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzf_24758/02_2024/7rzf_24758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzf_24758/02_2024/7rzf_24758.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzf_24758/02_2024/7rzf_24758.pdb" } resolution = 3.4 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 10044 2.51 5 N 2613 2.21 5 O 2882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 63": "OE1" <-> "OE2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 507": "OD1" <-> "OD2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A TYR 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A ASP 698": "OD1" <-> "OD2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ASP 747": "OD1" <-> "OD2" Residue "A TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 773": "OD1" <-> "OD2" Residue "A ARG 782": "NH1" <-> "NH2" Residue "A GLU 809": "OE1" <-> "OE2" Residue "A GLU 827": "OE1" <-> "OE2" Residue "A ARG 862": "NH1" <-> "NH2" Residue "A ASP 876": "OD1" <-> "OD2" Residue "A ARG 892": "NH1" <-> "NH2" Residue "A ASP 921": "OD1" <-> "OD2" Residue "A ASP 947": "OD1" <-> "OD2" Residue "A GLU 962": "OE1" <-> "OE2" Residue "A PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B GLU 458": "OE1" <-> "OE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 598": "OE1" <-> "OE2" Residue "B GLU 612": "OE1" <-> "OE2" Residue "B TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 653": "OE1" <-> "OE2" Residue "B ASP 655": "OD1" <-> "OD2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B ASP 698": "OD1" <-> "OD2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B GLU 768": "OE1" <-> "OE2" Residue "B ASP 773": "OD1" <-> "OD2" Residue "B TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 809": "OE1" <-> "OE2" Residue "B PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 862": "NH1" <-> "NH2" Residue "B GLU 880": "OE1" <-> "OE2" Residue "B PHE 882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 892": "NH1" <-> "NH2" Residue "B ASP 947": "OD1" <-> "OD2" Residue "B PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15584 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7763 Classifications: {'peptide': 948} Link IDs: {'PTRANS': 51, 'TRANS': 896} Chain breaks: 1 Chain: "B" Number of atoms: 7704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 940, 7704 Classifications: {'peptide': 940} Link IDs: {'PTRANS': 49, 'TRANS': 890} Chain breaks: 1 Chain: "a" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain breaks: 1 Chain: "b" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Time building chain proxies: 8.17, per 1000 atoms: 0.52 Number of scatterers: 15584 At special positions: 0 Unit cell: (156.125, 133.357, 116.009, 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 45 16.00 O 2882 8.00 N 2613 7.00 C 10044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS a 6 " - pdb=" SG CYS a 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.39 Conformation dependent library (CDL) restraints added in 3.0 seconds 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3628 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 13 sheets defined 45.2% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.624A pdb=" N SER A 98 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP A 99 " --> pdb=" O SER A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 95 through 99' Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.985A pdb=" N PHE A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 158 through 171 removed outlier: 4.514A pdb=" N ARG A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 194 removed outlier: 4.218A pdb=" N VAL A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 removed outlier: 3.524A pdb=" N ARG A 200 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 237 through 249 Processing helix chain 'A' and resid 267 through 273 removed outlier: 3.724A pdb=" N LYS A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.531A pdb=" N LEU A 298 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 345 through 353 removed outlier: 3.654A pdb=" N LEU A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 403 Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.683A pdb=" N PHE A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 440 removed outlier: 3.617A pdb=" N TYR A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER A 435 " --> pdb=" O ARG A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.802A pdb=" N ILE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 removed outlier: 3.904A pdb=" N ILE A 510 " --> pdb=" O PRO A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 615 removed outlier: 3.862A pdb=" N ALA A 593 " --> pdb=" O HIS A 589 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N TYR A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 removed outlier: 3.627A pdb=" N LEU A 641 " --> pdb=" O LYS A 637 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.725A pdb=" N GLU A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN A 671 " --> pdb=" O MET A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 677 through 690 removed outlier: 3.844A pdb=" N ARG A 687 " --> pdb=" O MET A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 removed outlier: 3.663A pdb=" N LYS A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 720 Proline residue: A 717 - end of helix Processing helix chain 'A' and resid 734 through 754 Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.630A pdb=" N LEU A 763 " --> pdb=" O PRO A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 3.954A pdb=" N LEU A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 824 removed outlier: 3.752A pdb=" N PHE A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 877 removed outlier: 3.520A pdb=" N LEU A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 894 removed outlier: 3.516A pdb=" N PHE A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 894 " --> pdb=" O ALA A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 912 removed outlier: 3.736A pdb=" N LYS A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU A 910 " --> pdb=" O LYS A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 929 Processing helix chain 'A' and resid 932 through 945 removed outlier: 3.846A pdb=" N ILE A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 945 " --> pdb=" O LYS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 999 Processing helix chain 'B' and resid 105 through 114 Processing helix chain 'B' and resid 125 through 134 removed outlier: 3.506A pdb=" N HIS B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 165 through 169 removed outlier: 3.720A pdb=" N PHE B 168 " --> pdb=" O PHE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 removed outlier: 4.269A pdb=" N ASN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 removed outlier: 3.639A pdb=" N ARG B 200 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 222 through 227 removed outlier: 3.599A pdb=" N LEU B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 227 " --> pdb=" O LYS B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 227' Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.620A pdb=" N GLN B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 248 removed outlier: 3.716A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 275 removed outlier: 3.756A pdb=" N LYS B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 removed outlier: 3.518A pdb=" N GLY B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 460 through 471 removed outlier: 3.624A pdb=" N ILE B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 515 removed outlier: 3.644A pdb=" N ILE B 510 " --> pdb=" O PRO B 506 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 514 " --> pdb=" O ILE B 510 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 515 " --> pdb=" O LYS B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 removed outlier: 3.997A pdb=" N TYR B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 584' Processing helix chain 'B' and resid 586 through 613 removed outlier: 4.928A pdb=" N GLU B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TYR B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 651 Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 673 through 676 removed outlier: 3.940A pdb=" N GLU B 676 " --> pdb=" O PHE B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 676' Processing helix chain 'B' and resid 677 through 691 Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.943A pdb=" N ASP B 705 " --> pdb=" O LYS B 701 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 722 Proline residue: B 717 - end of helix removed outlier: 4.303A pdb=" N ARG B 722 " --> pdb=" O GLN B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 754 Processing helix chain 'B' and resid 801 through 815 removed outlier: 4.081A pdb=" N MET B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 823 removed outlier: 3.520A pdb=" N ALA B 819 " --> pdb=" O ILE B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 876 removed outlier: 3.739A pdb=" N GLU B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 894 removed outlier: 3.693A pdb=" N PHE B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 912 removed outlier: 3.616A pdb=" N GLU B 903 " --> pdb=" O LYS B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 929 Processing helix chain 'B' and resid 932 through 945 removed outlier: 3.646A pdb=" N ILE B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU B 942 " --> pdb=" O LYS B 938 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET B 943 " --> pdb=" O PHE B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1001 removed outlier: 4.587A pdb=" N GLY B1001 " --> pdb=" O GLU B 997 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 removed outlier: 6.364A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 87 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 360 removed outlier: 4.492A pdb=" N PHE A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY A 366 " --> pdb=" O PHE A 370 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 359 through 360 Processing sheet with id=AA4, first strand: chain 'A' and resid 491 through 492 removed outlier: 3.731A pdb=" N ARG A 491 " --> pdb=" O TYR A 500 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 557 through 558 removed outlier: 6.124A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LYS A 562 " --> pdb=" O GLY A 731 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 557 through 558 removed outlier: 6.124A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS A 724 " --> pdb=" O PHE A 579 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 832 through 840 removed outlier: 4.561A pdb=" N ILE A 832 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 836 " --> pdb=" O ARG A 847 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLN A 844 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 778 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 63 through 69 removed outlier: 6.208A pdb=" N LYS B 74 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL B 258 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU B 76 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLY B 260 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE B 78 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 91 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 86 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 303 through 304 Processing sheet with id=AB1, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AB2, first strand: chain 'B' and resid 549 through 553 removed outlier: 6.011A pdb=" N LEU B 550 " --> pdb=" O PHE B 561 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N PHE B 561 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS B 558 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU B 729 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TRP B 560 " --> pdb=" O LEU B 729 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLY B 731 " --> pdb=" O TRP B 560 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LYS B 562 " --> pdb=" O GLY B 731 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 776 through 777 removed outlier: 6.189A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 776 through 777 removed outlier: 6.189A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLY B 790 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N SER B 852 " --> pdb=" O GLY B 790 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLU B 792 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE B 850 " --> pdb=" O GLU B 792 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR B 794 " --> pdb=" O PHE B 848 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE B 848 " --> pdb=" O TYR B 794 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN B 796 " --> pdb=" O LEU B 846 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU B 846 " --> pdb=" O GLN B 796 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP B 798 " --> pdb=" O GLN B 844 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE B 832 " --> pdb=" O GLN B 851 " (cutoff:3.500A) 677 hydrogen bonds defined for protein. 1950 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: 5.40 Time building geometry restraints manager: 5.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4371 1.33 - 1.45: 2822 1.45 - 1.57: 8688 1.57 - 1.69: 1 1.69 - 1.81: 88 Bond restraints: 15970 Sorted by residual: bond pdb=" N ASP B 586 " pdb=" CA ASP B 586 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.73e+01 bond pdb=" N ASP B 99 " pdb=" CA ASP B 99 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.73e+01 bond pdb=" N VAL B 707 " pdb=" CA VAL B 707 " ideal model delta sigma weight residual 1.457 1.497 -0.041 1.19e-02 7.06e+03 1.16e+01 bond pdb=" N ILE B 235 " pdb=" CA ILE B 235 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.19e-02 7.06e+03 9.66e+00 bond pdb=" N VAL B 769 " pdb=" CA VAL B 769 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.48e+00 ... (remaining 15965 not shown) Histogram of bond angle deviations from ideal: 95.08 - 102.92: 123 102.92 - 110.76: 5062 110.76 - 118.59: 7585 118.59 - 126.43: 8608 126.43 - 134.27: 213 Bond angle restraints: 21591 Sorted by residual: angle pdb=" N LEU B 763 " pdb=" CA LEU B 763 " pdb=" C LEU B 763 " ideal model delta sigma weight residual 112.57 103.72 8.85 1.13e+00 7.83e-01 6.13e+01 angle pdb=" N SER B 96 " pdb=" CA SER B 96 " pdb=" C SER B 96 " ideal model delta sigma weight residual 112.54 106.53 6.01 1.22e+00 6.72e-01 2.43e+01 angle pdb=" C ILE A 912 " pdb=" CA ILE A 912 " pdb=" CB ILE A 912 " ideal model delta sigma weight residual 111.29 103.29 8.00 1.64e+00 3.72e-01 2.38e+01 angle pdb=" C ALA A 367 " pdb=" CA ALA A 367 " pdb=" CB ALA A 367 " ideal model delta sigma weight residual 116.54 111.42 5.12 1.15e+00 7.56e-01 1.98e+01 angle pdb=" CA HIS B 291 " pdb=" C HIS B 291 " pdb=" O HIS B 291 " ideal model delta sigma weight residual 120.19 116.55 3.64 8.40e-01 1.42e+00 1.88e+01 ... (remaining 21586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8904 18.00 - 36.00: 625 36.00 - 53.99: 114 53.99 - 71.99: 17 71.99 - 89.99: 10 Dihedral angle restraints: 9670 sinusoidal: 4060 harmonic: 5610 Sorted by residual: dihedral pdb=" CA LYS A 511 " pdb=" C LYS A 511 " pdb=" N LYS A 512 " pdb=" CA LYS A 512 " ideal model delta harmonic sigma weight residual 180.00 154.42 25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLN B 800 " pdb=" C GLN B 800 " pdb=" N SER B 801 " pdb=" CA SER B 801 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ARG A 261 " pdb=" C ARG A 261 " pdb=" N GLU A 262 " pdb=" CA GLU A 262 " ideal model delta harmonic sigma weight residual -180.00 -155.50 -24.50 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 9667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1728 0.074 - 0.148: 509 0.148 - 0.223: 71 0.223 - 0.297: 8 0.297 - 0.371: 5 Chirality restraints: 2321 Sorted by residual: chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CG LEU B 77 " pdb=" CB LEU B 77 " pdb=" CD1 LEU B 77 " pdb=" CD2 LEU B 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA LEU B 763 " pdb=" N LEU B 763 " pdb=" C LEU B 763 " pdb=" CB LEU B 763 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 2318 not shown) Planarity restraints: 2791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 461 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C PRO B 461 " -0.058 2.00e-02 2.50e+03 pdb=" O PRO B 461 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP B 462 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 666 " 0.032 2.00e-02 2.50e+03 2.18e-02 9.53e+00 pdb=" CG TYR A 666 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 666 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 666 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 666 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 666 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 666 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 666 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 866 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.15e+00 pdb=" C PHE B 866 " -0.052 2.00e-02 2.50e+03 pdb=" O PHE B 866 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU B 867 " 0.018 2.00e-02 2.50e+03 ... (remaining 2788 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 6 2.14 - 2.83: 4881 2.83 - 3.52: 21112 3.52 - 4.21: 35831 4.21 - 4.90: 61454 Nonbonded interactions: 123284 Sorted by model distance: nonbonded pdb=" CZ ARG B 229 " pdb=" OE2 GLU B 233 " model vdw 1.454 3.270 nonbonded pdb=" NE ARG B 229 " pdb=" OE2 GLU B 233 " model vdw 1.702 2.520 nonbonded pdb=" NH2 ARG B 229 " pdb=" OE2 GLU B 233 " model vdw 1.711 2.520 nonbonded pdb=" O HIS A 134 " pdb=" OG SER A 154 " model vdw 2.090 2.440 nonbonded pdb=" OG1 THR A 623 " pdb=" O GLY A 626 " model vdw 2.136 2.440 ... (remaining 123279 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 'A' and (resid 47 through 962 or resid 989 through 1011)) selection = (chain 'B' and resid 47 through 1011) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.880 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 41.900 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 60.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 : 0.009 0.074 15970 Z= 0.549 Angle : 1.186 10.238 21591 Z= 0.680 Chirality : 0.069 0.371 2321 Planarity : 0.008 0.062 2791 Dihedral : 12.934 89.990 6039 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.41 % Allowed : 1.94 % Favored : 97.64 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.16), residues: 1889 helix: -3.00 (0.13), residues: 776 sheet: -1.87 (0.26), residues: 347 loop : -2.55 (0.19), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.004 TRP B 695 HIS 0.016 0.003 HIS A 589 PHE 0.047 0.004 PHE B 866 TYR 0.052 0.004 TYR A 666 ARG 0.027 0.002 ARG B 711 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 225 time to evaluate : 1.689 Fit side-chains revert: symmetry clash REVERT: A 358 THR cc_start: 0.7562 (t) cc_final: 0.7278 (m) REVERT: A 426 ASP cc_start: 0.7180 (p0) cc_final: 0.6958 (p0) REVERT: A 779 TYR cc_start: 0.6866 (p90) cc_final: 0.5855 (p90) REVERT: B 62 ARG cc_start: 0.3971 (mtm-85) cc_final: 0.3730 (mtm-85) REVERT: B 332 HIS cc_start: 0.5921 (t-90) cc_final: 0.5649 (t70) REVERT: B 429 ARG cc_start: 0.6480 (tpt-90) cc_final: 0.6009 (tpt90) REVERT: B 855 PRO cc_start: 0.7719 (Cg_exo) cc_final: 0.7479 (Cg_endo) REVERT: B 993 GLN cc_start: 0.7136 (mp10) cc_final: 0.6935 (mp10) outliers start: 7 outliers final: 2 residues processed: 229 average time/residue: 0.2752 time to fit residues: 93.7049 Evaluate side-chains 136 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 688 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 796 GLN ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 770 GLN B 844 GLN ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 GLN ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15970 Z= 0.176 Angle : 0.656 9.007 21591 Z= 0.339 Chirality : 0.044 0.173 2321 Planarity : 0.005 0.042 2791 Dihedral : 5.608 58.907 2067 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.30 % Allowed : 7.54 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.17), residues: 1889 helix: -1.18 (0.16), residues: 788 sheet: -1.43 (0.26), residues: 362 loop : -2.05 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 776 HIS 0.005 0.001 HIS A 589 PHE 0.031 0.002 PHE B 866 TYR 0.023 0.002 TYR A 594 ARG 0.018 0.001 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7324 (tpp) cc_final: 0.6790 (tpp) REVERT: A 145 GLU cc_start: 0.7546 (tp30) cc_final: 0.6819 (tp30) REVERT: A 426 ASP cc_start: 0.7245 (p0) cc_final: 0.7025 (p0) REVERT: A 723 LEU cc_start: 0.8448 (pp) cc_final: 0.8196 (pp) REVERT: A 742 MET cc_start: 0.7798 (tpp) cc_final: 0.7542 (tpp) REVERT: A 779 TYR cc_start: 0.6493 (p90) cc_final: 0.5791 (p90) REVERT: B 62 ARG cc_start: 0.4010 (mtm-85) cc_final: 0.3619 (mtm-85) REVERT: B 113 MET cc_start: 0.3331 (mmm) cc_final: 0.3070 (mmp) REVERT: B 253 LEU cc_start: 0.5035 (mt) cc_final: 0.4810 (mp) REVERT: B 299 LYS cc_start: 0.7075 (mtmt) cc_final: 0.6835 (pttp) REVERT: B 332 HIS cc_start: 0.5984 (t-90) cc_final: 0.5737 (t70) REVERT: B 429 ARG cc_start: 0.6136 (tpt-90) cc_final: 0.5672 (tpt90) REVERT: B 627 MET cc_start: 0.6081 (ttm) cc_final: 0.5771 (ttp) REVERT: B 744 MET cc_start: 0.7790 (tmm) cc_final: 0.7486 (tmm) REVERT: B 855 PRO cc_start: 0.7505 (Cg_exo) cc_final: 0.7132 (Cg_endo) REVERT: B 857 HIS cc_start: 0.6696 (OUTLIER) cc_final: 0.6139 (p-80) REVERT: B 870 MET cc_start: 0.7020 (mpp) cc_final: 0.6382 (mmm) REVERT: B 917 ASN cc_start: 0.6965 (t0) cc_final: 0.6724 (t0) outliers start: 22 outliers final: 15 residues processed: 198 average time/residue: 0.2424 time to fit residues: 75.9657 Evaluate side-chains 160 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain b residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 142 optimal weight: 0.0980 chunk 116 optimal weight: 20.0000 chunk 47 optimal weight: 0.0270 chunk 171 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 overall best weight: 1.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS B 245 HIS ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15970 Z= 0.235 Angle : 0.640 7.674 21591 Z= 0.329 Chirality : 0.045 0.177 2321 Planarity : 0.004 0.039 2791 Dihedral : 5.194 20.298 2065 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.00 % Allowed : 10.19 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.18), residues: 1889 helix: -0.31 (0.18), residues: 791 sheet: -1.08 (0.25), residues: 375 loop : -1.85 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 776 HIS 0.007 0.001 HIS A 589 PHE 0.036 0.002 PHE B 866 TYR 0.023 0.002 TYR A 666 ARG 0.004 0.001 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 162 time to evaluate : 1.831 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.7481 (tpp) cc_final: 0.6959 (tpp) REVERT: A 145 GLU cc_start: 0.7315 (tp30) cc_final: 0.6462 (tp30) REVERT: A 224 TYR cc_start: 0.7871 (t80) cc_final: 0.7526 (t80) REVERT: A 394 MET cc_start: 0.7347 (mtt) cc_final: 0.7133 (mtt) REVERT: A 514 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7213 (pt0) REVERT: A 779 TYR cc_start: 0.6608 (p90) cc_final: 0.5347 (p90) REVERT: A 877 MET cc_start: 0.7097 (ppp) cc_final: 0.6864 (ppp) REVERT: B 62 ARG cc_start: 0.4039 (mtm-85) cc_final: 0.3305 (mpp80) REVERT: B 267 LEU cc_start: 0.4004 (OUTLIER) cc_final: 0.3697 (mt) REVERT: B 429 ARG cc_start: 0.6423 (tpt-90) cc_final: 0.5997 (tpt90) REVERT: B 744 MET cc_start: 0.7832 (tmm) cc_final: 0.7619 (tmm) REVERT: B 857 HIS cc_start: 0.6473 (OUTLIER) cc_final: 0.5973 (p-80) REVERT: B 866 PHE cc_start: 0.8713 (t80) cc_final: 0.7594 (t80) REVERT: B 870 MET cc_start: 0.7430 (mpp) cc_final: 0.7001 (mmm) REVERT: B 917 ASN cc_start: 0.7053 (t0) cc_final: 0.6761 (t0) REVERT: b 1 PHE cc_start: 0.5719 (t80) cc_final: 0.5417 (t80) outliers start: 34 outliers final: 24 residues processed: 188 average time/residue: 0.2490 time to fit residues: 72.9495 Evaluate side-chains 166 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 875 GLU Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain b residue 2 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 181 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 162 optimal weight: 0.7980 chunk 48 optimal weight: 0.0170 overall best weight: 1.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 HIS A 982 GLN B 502 GLN ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 ASN B 844 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15970 Z= 0.193 Angle : 0.584 7.655 21591 Z= 0.299 Chirality : 0.043 0.207 2321 Planarity : 0.004 0.038 2791 Dihedral : 4.952 19.227 2065 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.59 % Allowed : 11.02 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.19), residues: 1889 helix: 0.15 (0.18), residues: 797 sheet: -0.62 (0.26), residues: 362 loop : -1.70 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 355 HIS 0.006 0.001 HIS A 957 PHE 0.032 0.001 PHE B 866 TYR 0.021 0.002 TYR A 779 ARG 0.006 0.000 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 161 time to evaluate : 1.705 Fit side-chains revert: symmetry clash REVERT: A 145 GLU cc_start: 0.7229 (tp30) cc_final: 0.6501 (tp30) REVERT: A 168 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.5570 (t80) REVERT: A 699 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6830 (mt-10) REVERT: A 749 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8212 (mt) REVERT: A 779 TYR cc_start: 0.6806 (p90) cc_final: 0.5504 (p90) REVERT: A 982 GLN cc_start: 0.6869 (tp40) cc_final: 0.6602 (tp40) REVERT: B 267 LEU cc_start: 0.3977 (OUTLIER) cc_final: 0.3722 (mt) REVERT: B 470 LYS cc_start: 0.8431 (tppt) cc_final: 0.8023 (mtmm) REVERT: B 857 HIS cc_start: 0.6491 (OUTLIER) cc_final: 0.5989 (p-80) REVERT: B 866 PHE cc_start: 0.8787 (t80) cc_final: 0.7725 (t80) REVERT: B 870 MET cc_start: 0.7269 (mpp) cc_final: 0.7036 (mmm) REVERT: B 917 ASN cc_start: 0.7071 (t0) cc_final: 0.6781 (t0) REVERT: B 943 MET cc_start: 0.8005 (mmt) cc_final: 0.7755 (mmt) REVERT: b 1 PHE cc_start: 0.5675 (t80) cc_final: 0.5362 (t80) outliers start: 44 outliers final: 29 residues processed: 192 average time/residue: 0.2464 time to fit residues: 73.0672 Evaluate side-chains 171 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain b residue 2 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 157 HIS A 514 GLN A 732 ASN ** B 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 15970 Z= 0.300 Angle : 0.673 7.751 21591 Z= 0.343 Chirality : 0.045 0.160 2321 Planarity : 0.005 0.045 2791 Dihedral : 5.229 21.115 2065 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.36 % Allowed : 12.61 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1889 helix: 0.17 (0.18), residues: 792 sheet: -0.64 (0.26), residues: 371 loop : -1.78 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 776 HIS 0.013 0.002 HIS A 957 PHE 0.034 0.002 PHE B 866 TYR 0.025 0.002 TYR A 779 ARG 0.007 0.001 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 152 time to evaluate : 1.901 Fit side-chains revert: symmetry clash REVERT: A 145 GLU cc_start: 0.7379 (tp30) cc_final: 0.6663 (tp30) REVERT: A 168 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.5856 (t80) REVERT: A 1011 HIS cc_start: 0.6064 (t-170) cc_final: 0.5856 (t-170) REVERT: B 92 VAL cc_start: 0.7789 (m) cc_final: 0.7275 (p) REVERT: B 254 MET cc_start: 0.5729 (tmm) cc_final: 0.5393 (mmt) REVERT: B 470 LYS cc_start: 0.8388 (tppt) cc_final: 0.8025 (mtmm) REVERT: B 702 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: B 857 HIS cc_start: 0.6606 (OUTLIER) cc_final: 0.6119 (p-80) REVERT: B 870 MET cc_start: 0.7474 (mpp) cc_final: 0.6953 (mmm) REVERT: B 917 ASN cc_start: 0.6995 (t0) cc_final: 0.6694 (t0) REVERT: B 943 MET cc_start: 0.7921 (mmt) cc_final: 0.7693 (mmt) REVERT: b 5 HIS cc_start: 0.5873 (OUTLIER) cc_final: 0.5149 (m-70) outliers start: 57 outliers final: 40 residues processed: 195 average time/residue: 0.2651 time to fit residues: 84.4687 Evaluate side-chains 187 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 143 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 5 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.3980 chunk 163 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 982 GLN B 108 HIS ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 ASN ** B 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15970 Z= 0.228 Angle : 0.615 9.530 21591 Z= 0.312 Chirality : 0.044 0.143 2321 Planarity : 0.004 0.037 2791 Dihedral : 5.073 20.681 2065 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.18 % Allowed : 13.20 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.19), residues: 1889 helix: 0.40 (0.18), residues: 789 sheet: -0.50 (0.26), residues: 365 loop : -1.79 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 355 HIS 0.009 0.001 HIS b 5 PHE 0.031 0.001 PHE B 866 TYR 0.021 0.002 TYR A 779 ARG 0.005 0.001 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 148 time to evaluate : 1.935 Fit side-chains REVERT: A 145 GLU cc_start: 0.7481 (tp30) cc_final: 0.6902 (tp30) REVERT: A 168 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.5854 (t80) REVERT: A 982 GLN cc_start: 0.6886 (tp40) cc_final: 0.6642 (tp40) REVERT: A 990 GLU cc_start: 0.7463 (pm20) cc_final: 0.7049 (pm20) REVERT: B 71 ASN cc_start: 0.1803 (OUTLIER) cc_final: 0.1381 (p0) REVERT: B 92 VAL cc_start: 0.7648 (m) cc_final: 0.7304 (p) REVERT: B 254 MET cc_start: 0.5708 (tmm) cc_final: 0.5378 (mmt) REVERT: B 465 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: B 470 LYS cc_start: 0.8328 (tppt) cc_final: 0.8010 (mtmm) REVERT: B 676 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6473 (tt0) REVERT: B 702 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: B 857 HIS cc_start: 0.6635 (OUTLIER) cc_final: 0.6144 (p-80) REVERT: B 917 ASN cc_start: 0.6948 (t0) cc_final: 0.6670 (t0) REVERT: B 943 MET cc_start: 0.7963 (mmt) cc_final: 0.7736 (mmt) REVERT: b 5 HIS cc_start: 0.5521 (OUTLIER) cc_final: 0.4741 (m-70) outliers start: 54 outliers final: 40 residues processed: 191 average time/residue: 0.2358 time to fit residues: 71.8522 Evaluate side-chains 186 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 139 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 5 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 132 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 110 optimal weight: 30.0000 chunk 83 optimal weight: 6.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN B 108 HIS ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 752 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15970 Z= 0.404 Angle : 0.761 10.113 21591 Z= 0.387 Chirality : 0.048 0.186 2321 Planarity : 0.005 0.044 2791 Dihedral : 5.564 22.428 2065 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.71 % Allowed : 13.55 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 1889 helix: -0.07 (0.18), residues: 792 sheet: -0.57 (0.26), residues: 363 loop : -2.02 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 355 HIS 0.020 0.002 HIS b 5 PHE 0.044 0.002 PHE B 866 TYR 0.029 0.003 TYR A 779 ARG 0.008 0.001 ARG A 847 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 136 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 HIS cc_start: 0.7402 (OUTLIER) cc_final: 0.6771 (m170) REVERT: A 168 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.5984 (t80) REVERT: A 844 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6817 (pm20) REVERT: A 952 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.7563 (m-70) REVERT: B 71 ASN cc_start: 0.2500 (OUTLIER) cc_final: 0.2031 (p0) REVERT: B 92 VAL cc_start: 0.7716 (m) cc_final: 0.7298 (p) REVERT: B 254 MET cc_start: 0.5763 (tmm) cc_final: 0.5511 (mmt) REVERT: B 470 LYS cc_start: 0.8513 (tppt) cc_final: 0.8140 (mtmm) REVERT: B 676 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6453 (tt0) REVERT: B 857 HIS cc_start: 0.6608 (OUTLIER) cc_final: 0.6265 (p-80) REVERT: B 870 MET cc_start: 0.7643 (mpp) cc_final: 0.7145 (mmm) REVERT: B 943 MET cc_start: 0.7932 (mmt) cc_final: 0.7729 (mmt) REVERT: b 1 PHE cc_start: 0.5652 (t80) cc_final: 0.5092 (t80) outliers start: 63 outliers final: 49 residues processed: 185 average time/residue: 0.2318 time to fit residues: 68.5345 Evaluate side-chains 184 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 128 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 844 GLN Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 952 HIS Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain b residue 2 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 142 optimal weight: 0.0570 chunk 164 optimal weight: 6.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 982 GLN ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15970 Z= 0.224 Angle : 0.628 10.412 21591 Z= 0.318 Chirality : 0.044 0.173 2321 Planarity : 0.004 0.054 2791 Dihedral : 5.195 20.161 2065 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.71 % Allowed : 13.44 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.19), residues: 1889 helix: 0.31 (0.18), residues: 789 sheet: -0.48 (0.26), residues: 361 loop : -1.95 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 355 HIS 0.008 0.001 HIS A 957 PHE 0.035 0.002 PHE B 866 TYR 0.020 0.002 TYR A 779 ARG 0.005 0.001 ARG A 477 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 147 time to evaluate : 1.868 Fit side-chains revert: symmetry clash REVERT: A 145 GLU cc_start: 0.7294 (tp30) cc_final: 0.6620 (tp30) REVERT: A 168 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.5993 (t80) REVERT: A 483 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7030 (tppt) REVERT: A 742 MET cc_start: 0.7787 (tpp) cc_final: 0.7390 (tpp) REVERT: A 779 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.5967 (p90) REVERT: A 959 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7051 (pp) REVERT: A 982 GLN cc_start: 0.6935 (tp40) cc_final: 0.6695 (tp40) REVERT: A 990 GLU cc_start: 0.7476 (pm20) cc_final: 0.7169 (pm20) REVERT: B 71 ASN cc_start: 0.2193 (OUTLIER) cc_final: 0.1689 (p0) REVERT: B 92 VAL cc_start: 0.7627 (m) cc_final: 0.7192 (p) REVERT: B 162 LEU cc_start: 0.5162 (tp) cc_final: 0.4405 (mt) REVERT: B 254 MET cc_start: 0.5699 (tmm) cc_final: 0.5465 (mmt) REVERT: B 267 LEU cc_start: 0.3370 (OUTLIER) cc_final: 0.2989 (mt) REVERT: B 470 LYS cc_start: 0.8484 (tppt) cc_final: 0.8250 (mtmt) REVERT: B 676 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6499 (tt0) REVERT: B 857 HIS cc_start: 0.6593 (OUTLIER) cc_final: 0.6280 (p-80) REVERT: B 870 MET cc_start: 0.7604 (mpp) cc_final: 0.7216 (mmm) REVERT: B 943 MET cc_start: 0.7998 (mmt) cc_final: 0.7785 (mmt) REVERT: b 1 PHE cc_start: 0.5570 (t80) cc_final: 0.4991 (t80) outliers start: 63 outliers final: 50 residues processed: 193 average time/residue: 0.2505 time to fit residues: 75.1591 Evaluate side-chains 202 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 144 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 903 GLU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain b residue 2 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 110 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15970 Z= 0.160 Angle : 0.576 9.962 21591 Z= 0.293 Chirality : 0.043 0.181 2321 Planarity : 0.004 0.042 2791 Dihedral : 4.840 19.525 2065 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.01 % Allowed : 14.08 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1889 helix: 0.67 (0.19), residues: 789 sheet: -0.42 (0.26), residues: 364 loop : -1.75 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 355 HIS 0.005 0.001 HIS A 957 PHE 0.032 0.001 PHE B 866 TYR 0.014 0.001 TYR A 779 ARG 0.006 0.000 ARG B 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 152 time to evaluate : 1.673 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.7276 (tpp) cc_final: 0.7058 (mpp) REVERT: A 145 GLU cc_start: 0.7301 (tp30) cc_final: 0.6604 (tp30) REVERT: A 168 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.5984 (t80) REVERT: A 413 GLU cc_start: 0.7861 (tp30) cc_final: 0.7508 (tt0) REVERT: A 598 GLU cc_start: 0.6569 (mm-30) cc_final: 0.6347 (mm-30) REVERT: A 742 MET cc_start: 0.7981 (tpp) cc_final: 0.7584 (tpp) REVERT: A 779 TYR cc_start: 0.7136 (OUTLIER) cc_final: 0.5932 (p90) REVERT: A 959 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7169 (pp) REVERT: A 982 GLN cc_start: 0.6939 (tp40) cc_final: 0.6699 (tp40) REVERT: B 71 ASN cc_start: 0.1847 (OUTLIER) cc_final: 0.1383 (p0) REVERT: B 92 VAL cc_start: 0.7614 (m) cc_final: 0.7056 (p) REVERT: B 267 LEU cc_start: 0.3187 (OUTLIER) cc_final: 0.2832 (mt) REVERT: B 430 PRO cc_start: 0.4202 (Cg_exo) cc_final: 0.3899 (Cg_endo) REVERT: B 470 LYS cc_start: 0.8415 (tppt) cc_final: 0.8210 (mtmt) REVERT: B 746 GLU cc_start: 0.6364 (pt0) cc_final: 0.6019 (mt-10) REVERT: B 808 LEU cc_start: 0.8472 (tp) cc_final: 0.8178 (tp) REVERT: B 857 HIS cc_start: 0.6572 (OUTLIER) cc_final: 0.6185 (p-80) REVERT: B 870 MET cc_start: 0.7511 (mpp) cc_final: 0.7148 (mmm) REVERT: B 917 ASN cc_start: 0.6889 (t0) cc_final: 0.6618 (t0) REVERT: B 943 MET cc_start: 0.7959 (mmt) cc_final: 0.7740 (mmt) REVERT: b 1 PHE cc_start: 0.5598 (t80) cc_final: 0.4986 (t80) outliers start: 51 outliers final: 42 residues processed: 190 average time/residue: 0.2492 time to fit residues: 73.9394 Evaluate side-chains 190 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 142 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain b residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 115 optimal weight: 0.0270 chunk 91 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 158 optimal weight: 0.4980 overall best weight: 2.1044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15970 Z= 0.251 Angle : 0.642 10.587 21591 Z= 0.325 Chirality : 0.044 0.179 2321 Planarity : 0.004 0.041 2791 Dihedral : 5.029 19.701 2065 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.30 % Allowed : 14.14 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.19), residues: 1889 helix: 0.51 (0.18), residues: 793 sheet: -0.41 (0.26), residues: 362 loop : -1.84 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 776 HIS 0.009 0.001 HIS A 957 PHE 0.038 0.002 PHE B 866 TYR 0.019 0.002 TYR A 779 ARG 0.004 0.001 ARG A 838 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3778 Ramachandran restraints generated. 1889 Oldfield, 0 Emsley, 1889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 137 time to evaluate : 1.691 Fit side-chains revert: symmetry clash REVERT: A 112 HIS cc_start: 0.7476 (OUTLIER) cc_final: 0.6778 (m170) REVERT: A 113 MET cc_start: 0.7365 (tpp) cc_final: 0.7059 (mpp) REVERT: A 145 GLU cc_start: 0.7290 (tp30) cc_final: 0.6588 (tp30) REVERT: A 168 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6006 (t80) REVERT: A 779 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.5935 (p90) REVERT: A 877 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7111 (ppp) REVERT: A 959 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7122 (pp) REVERT: A 982 GLN cc_start: 0.6957 (tp40) cc_final: 0.6703 (tp40) REVERT: B 71 ASN cc_start: 0.2171 (OUTLIER) cc_final: 0.1675 (p0) REVERT: B 267 LEU cc_start: 0.3485 (OUTLIER) cc_final: 0.3042 (mt) REVERT: B 279 GLU cc_start: 0.4550 (pm20) cc_final: 0.4128 (pm20) REVERT: B 371 MET cc_start: 0.2841 (mtm) cc_final: 0.2627 (mtm) REVERT: B 430 PRO cc_start: 0.4256 (Cg_exo) cc_final: 0.3962 (Cg_endo) REVERT: B 470 LYS cc_start: 0.8513 (tppt) cc_final: 0.8303 (mtmt) REVERT: B 649 MET cc_start: 0.7337 (ttp) cc_final: 0.7014 (ttm) REVERT: B 857 HIS cc_start: 0.6489 (OUTLIER) cc_final: 0.6198 (p-80) REVERT: B 870 MET cc_start: 0.7639 (mpp) cc_final: 0.7352 (mmm) REVERT: B 943 MET cc_start: 0.8003 (mmt) cc_final: 0.7795 (mmt) REVERT: b 1 PHE cc_start: 0.5616 (t80) cc_final: 0.5024 (t80) outliers start: 56 outliers final: 45 residues processed: 179 average time/residue: 0.2608 time to fit residues: 75.1840 Evaluate side-chains 185 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 132 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 249 TYR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 297 HIS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 779 TYR Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 355 TRP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 698 ASP Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 755 THR Chi-restraints excluded: chain B residue 813 GLN Chi-restraints excluded: chain B residue 814 ILE Chi-restraints excluded: chain B residue 857 HIS Chi-restraints excluded: chain B residue 903 GLU Chi-restraints excluded: chain b residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 4.9990 chunk 137 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN ** B 514 GLN ** 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 = 0.4122 r_free = 0.4122 target = 0.137729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.105418 restraints weight = 31506.917| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.39 r_work: 0.3419 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15970 Z= 0.164 Angle : 0.578 9.987 21591 Z= 0.293 Chirality : 0.043 0.176 2321 Planarity : 0.004 0.043 2791 Dihedral : 4.810 19.338 2065 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.12 % Allowed : 14.14 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1889 helix: 0.75 (0.19), residues: 790 sheet: -0.38 (0.26), residues: 365 loop : -1.67 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 355 HIS 0.005 0.001 HIS A 957 PHE 0.032 0.001 PHE B 866 TYR 0.018 0.001 TYR A 594 ARG 0.005 0.000 ARG A 477 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3154.08 seconds wall clock time: 58 minutes 23.90 seconds (3503.90 seconds total)