Starting phenix.real_space_refine on Sun Dec 10 20:50:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzf_24758/12_2023/7rzf_24758.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzf_24758/12_2023/7rzf_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_24758/12_2023/7rzf_24758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzf_24758/12_2023/7rzf_24758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzf_24758/12_2023/7rzf_24758.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzf_24758/12_2023/7rzf_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 9.08, per 1000 atoms: 0.58 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: 7.87 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: 1.80 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: 5.68 Time building geometry restraints manager: 8.28 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: 3.190 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: 11.040 Check model and map are aligned: 0.240 Set scattering table: 0.130 Process input model: 47.270 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.080 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.010 ------------------------------------------------------------------------------- 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 : 2.098 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 229 average time/residue: 0.2801 time to fit residues: 95.9830 Evaluate side-chains 132 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.858 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1354 time to fit residues: 3.1321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7269 moved from start: 0.1647 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= 0.173 Angle : 0.649 8.604 21591 Z= 0.335 Chirality : 0.044 0.174 2321 Planarity : 0.005 0.041 2791 Dihedral : 5.423 21.396 2064 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.18 % Allowed : 7.78 % Favored : 91.04 % 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: -2.37 (0.17), residues: 1889 helix: -1.12 (0.17), residues: 787 sheet: -1.36 (0.26), residues: 359 loop : -2.02 (0.20), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 776 HIS 0.005 0.001 HIS A 589 PHE 0.030 0.002 PHE B 866 TYR 0.023 0.002 TYR A 594 ARG 0.005 0.001 ARG A 477 *********************** 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 206 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 199 average time/residue: 0.2399 time to fit residues: 75.6467 Evaluate side-chains 157 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 1.924 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1736 time to fit residues: 6.8051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 142 optimal weight: 0.0000 chunk 116 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 171 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 137 optimal weight: 20.0000 overall best weight: 2.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 157 HIS ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS B 245 HIS ** 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 844 GLN ** b 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15970 Z= 0.353 Angle : 0.736 8.346 21591 Z= 0.379 Chirality : 0.048 0.189 2321 Planarity : 0.005 0.039 2791 Dihedral : 5.503 20.131 2064 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.65 % Allowed : 10.78 % Favored : 87.57 % 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: -1.84 (0.18), residues: 1889 helix: -0.47 (0.17), residues: 790 sheet: -1.17 (0.25), residues: 381 loop : -1.96 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 776 HIS 0.011 0.002 HIS A 957 PHE 0.024 0.002 PHE B 578 TYR 0.028 0.003 TYR B 596 ARG 0.007 0.001 ARG A 261 *********************** 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 194 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 166 time to evaluate : 1.880 Fit side-chains outliers start: 28 outliers final: 13 residues processed: 188 average time/residue: 0.2931 time to fit residues: 85.3045 Evaluate side-chains 154 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 2.031 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1643 time to fit residues: 6.7914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 114 optimal weight: 40.0000 chunk 171 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 332 HIS A 732 ASN A 982 GLN B 108 HIS ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 ASN b 3 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2780 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= 0.226 Angle : 0.618 8.444 21591 Z= 0.317 Chirality : 0.044 0.245 2321 Planarity : 0.004 0.044 2791 Dihedral : 5.167 19.272 2064 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.12 % Allowed : 11.55 % Favored : 86.33 % 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: -1.30 (0.18), residues: 1889 helix: 0.05 (0.18), residues: 789 sheet: -0.73 (0.26), residues: 363 loop : -1.88 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 776 HIS 0.008 0.001 HIS A 957 PHE 0.022 0.001 PHE A 168 TYR 0.018 0.002 TYR A 779 ARG 0.007 0.001 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 204 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 168 time to evaluate : 1.742 Fit side-chains outliers start: 36 outliers final: 19 residues processed: 190 average time/residue: 0.2578 time to fit residues: 76.8634 Evaluate side-chains 162 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 2.054 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1466 time to fit residues: 7.7300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 2 optimal weight: 8.9990 chunk 135 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 125 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 502 GLN B 108 HIS ** B 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 ASN ** B 752 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15970 Z= 0.359 Angle : 0.737 9.402 21591 Z= 0.375 Chirality : 0.047 0.202 2321 Planarity : 0.005 0.046 2791 Dihedral : 5.534 21.860 2064 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.83 % Allowed : 13.44 % Favored : 84.74 % 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: -1.47 (0.18), residues: 1889 helix: -0.12 (0.18), residues: 790 sheet: -0.68 (0.26), residues: 365 loop : -2.01 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 776 HIS 0.014 0.002 HIS A 957 PHE 0.032 0.002 PHE B 578 TYR 0.023 0.003 TYR B 596 ARG 0.006 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 181 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 150 time to evaluate : 1.981 Fit side-chains outliers start: 31 outliers final: 11 residues processed: 177 average time/residue: 0.2680 time to fit residues: 74.7321 Evaluate side-chains 147 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 1.933 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1577 time to fit residues: 5.7618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 181 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15970 Z= 0.211 Angle : 0.622 8.629 21591 Z= 0.316 Chirality : 0.043 0.144 2321 Planarity : 0.004 0.051 2791 Dihedral : 5.176 21.400 2064 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.94 % Allowed : 15.20 % Favored : 83.85 % 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: -1.13 (0.19), residues: 1889 helix: 0.23 (0.18), residues: 795 sheet: -0.53 (0.26), residues: 365 loop : -1.92 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 355 HIS 0.006 0.001 HIS A 93 PHE 0.017 0.001 PHE B 578 TYR 0.014 0.002 TYR A 596 ARG 0.005 0.000 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 165 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 1.869 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 161 average time/residue: 0.2608 time to fit residues: 66.4405 Evaluate side-chains 143 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.959 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1609 time to fit residues: 5.2531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 103 optimal weight: 0.0980 chunk 132 optimal weight: 0.0020 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 110 optimal weight: 30.0000 chunk 83 optimal weight: 3.9990 overall best weight: 1.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 HIS B 502 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3568 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= 0.195 Angle : 0.601 8.815 21591 Z= 0.304 Chirality : 0.043 0.194 2321 Planarity : 0.004 0.042 2791 Dihedral : 5.018 22.223 2064 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.71 % Allowed : 15.56 % Favored : 83.74 % 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: -0.83 (0.19), residues: 1889 helix: 0.48 (0.19), residues: 787 sheet: -0.25 (0.27), residues: 353 loop : -1.79 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 355 HIS 0.006 0.001 HIS A 957 PHE 0.019 0.001 PHE A 109 TYR 0.017 0.002 TYR A 224 ARG 0.005 0.000 ARG A 477 *********************** 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 161 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 1.907 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 158 average time/residue: 0.2524 time to fit residues: 63.3532 Evaluate side-chains 140 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2071 time to fit residues: 4.9138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 0.0970 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 164 optimal weight: 0.0870 overall best weight: 2.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN B 752 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15970 Z= 0.318 Angle : 0.695 8.769 21591 Z= 0.353 Chirality : 0.046 0.237 2321 Planarity : 0.005 0.045 2791 Dihedral : 5.309 28.319 2064 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.59 % Allowed : 15.50 % Favored : 83.91 % 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: -1.12 (0.19), residues: 1889 helix: 0.22 (0.18), residues: 792 sheet: -0.40 (0.27), residues: 351 loop : -1.94 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 776 HIS 0.009 0.001 HIS A 957 PHE 0.027 0.002 PHE B 578 TYR 0.021 0.002 TYR A 596 ARG 0.005 0.001 ARG B 431 *********************** 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 152 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 2.017 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 147 average time/residue: 0.2540 time to fit residues: 59.9421 Evaluate side-chains 144 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 1.958 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1518 time to fit residues: 4.6685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 159 optimal weight: 0.1980 chunk 110 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15970 Z= 0.158 Angle : 0.594 9.268 21591 Z= 0.298 Chirality : 0.043 0.224 2321 Planarity : 0.004 0.042 2791 Dihedral : 4.895 26.921 2064 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.53 % Allowed : 15.79 % Favored : 83.68 % 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: -0.64 (0.19), residues: 1889 helix: 0.67 (0.19), residues: 784 sheet: -0.17 (0.27), residues: 355 loop : -1.72 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 355 HIS 0.004 0.001 HIS A 297 PHE 0.018 0.001 PHE A 109 TYR 0.019 0.001 TYR A 224 ARG 0.004 0.000 ARG A 477 *********************** 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 159 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 1.878 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 156 average time/residue: 0.2757 time to fit residues: 66.1721 Evaluate side-chains 139 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 2.058 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1890 time to fit residues: 3.5132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15970 Z= 0.309 Angle : 0.698 8.904 21591 Z= 0.352 Chirality : 0.046 0.235 2321 Planarity : 0.005 0.055 2791 Dihedral : 5.217 28.615 2064 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.29 % Allowed : 16.09 % 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: -0.98 (0.19), residues: 1889 helix: 0.37 (0.19), residues: 786 sheet: -0.41 (0.27), residues: 352 loop : -1.84 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 355 HIS 0.010 0.001 HIS A 957 PHE 0.028 0.002 PHE A 109 TYR 0.025 0.002 TYR A 594 ARG 0.006 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 140 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 2.259 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 137 average time/residue: 0.2592 time to fit residues: 56.8265 Evaluate side-chains 131 residues out of total 1697 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.875 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1464 time to fit residues: 2.8602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 22 optimal weight: 0.0020 chunk 41 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.138966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.105080 restraints weight = 31783.102| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 3.21 r_work: 0.3454 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4031 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= 0.164 Angle : 0.597 9.315 21591 Z= 0.301 Chirality : 0.043 0.294 2321 Planarity : 0.004 0.041 2791 Dihedral : 4.909 27.628 2064 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.12 % Allowed : 16.26 % 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: -0.67 (0.19), residues: 1889 helix: 0.65 (0.19), residues: 786 sheet: -0.28 (0.27), residues: 347 loop : -1.68 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 355 HIS 0.004 0.001 HIS A 957 PHE 0.023 0.001 PHE A 109 TYR 0.019 0.002 TYR A 224 ARG 0.006 0.000 ARG A 311 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3182.69 seconds wall clock time: 58 minutes 47.25 seconds (3527.25 seconds total)