Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 23:57:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rze_24757/07_2023/7rze_24757.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rze_24757/07_2023/7rze_24757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rze_24757/07_2023/7rze_24757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rze_24757/07_2023/7rze_24757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rze_24757/07_2023/7rze_24757.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rze_24757/07_2023/7rze_24757.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.007 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 44 5.16 5 C 10017 2.51 5 N 2606 2.21 5 O 2878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A ASP 773": "OD1" <-> "OD2" Residue "A ARG 782": "NH1" <-> "NH2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A GLU 827": "OE1" <-> "OE2" Residue "A ARG 862": "NH1" <-> "NH2" Residue "A ARG 892": "NH1" <-> "NH2" Residue "A PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B GLU 290": "OE1" <-> "OE2" Residue "B GLU 349": "OE1" <-> "OE2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B GLU 529": "OE1" <-> "OE2" Residue "B PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 577": "OE1" <-> "OE2" Residue "B GLU 612": "OE1" <-> "OE2" Residue "B GLU 660": "OE1" <-> "OE2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B ASP 773": "OD1" <-> "OD2" Residue "B GLU 784": "OE1" <-> "OE2" Residue "B ARG 862": "NH1" <-> "NH2" Residue "B GLU 864": "OE1" <-> "OE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B ARG 892": "NH1" <-> "NH2" Residue "B GLU 903": "OE1" <-> "OE2" Residue "B GLU 924": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "b PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 15545 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 947, 7749 Classifications: {'peptide': 947} Link IDs: {'PTRANS': 51, 'TRANS': 895} Chain breaks: 2 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: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "b" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Time building chain proxies: 7.59, per 1000 atoms: 0.49 Number of scatterers: 15545 At special positions: 0 Unit cell: (113.841, 124.683, 147.451, 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 44 16.00 O 2878 8.00 N 2606 7.00 C 10017 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 5.77 Conformation dependent library (CDL) restraints added in 2.5 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3620 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 45.6% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.614A pdb=" N SER A 98 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 3.954A 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: 3.874A 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: 4.447A pdb=" N ARG A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 193 removed outlier: 4.224A pdb=" N VAL A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 removed outlier: 3.548A pdb=" N THR A 208 " --> pdb=" O LEU A 204 " (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: 3.740A pdb=" N LYS A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.533A 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: 3.744A 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: 3.699A pdb=" N PHE A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 440 removed outlier: 3.622A pdb=" N TYR A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER A 435 " --> pdb=" O ARG A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.848A pdb=" N ILE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 removed outlier: 4.128A pdb=" N ILE A 510 " --> pdb=" O PRO A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 615 removed outlier: 4.030A pdb=" N ALA A 593 " --> pdb=" O HIS A 589 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N TYR A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ALA A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 removed outlier: 3.752A pdb=" N LEU A 641 " --> pdb=" O LYS A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.844A pdb=" N GLU A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 3.614A 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 Processing helix chain 'A' and resid 696 through 701 removed outlier: 3.703A pdb=" N LEU A 700 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 696 through 701' Processing helix chain 'A' and resid 708 through 714 Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'A' and resid 734 through 754 Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.725A pdb=" N LEU A 763 " --> pdb=" O PRO A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 3.813A pdb=" N LEU A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 824 removed outlier: 3.858A pdb=" N PHE A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 877 removed outlier: 3.542A pdb=" N LEU A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 877 " --> pdb=" O SER A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 893 Processing helix chain 'A' and resid 899 through 912 removed outlier: 3.558A pdb=" N GLU A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 4.111A 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 944 removed outlier: 3.501A pdb=" N ILE A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1001 removed outlier: 3.618A pdb=" N PHE A 998 " --> pdb=" O ASN A 994 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A1001 " --> pdb=" O GLU A 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.768A pdb=" N ASP B 99 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 114 removed outlier: 3.640A pdb=" N PHE B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.851A pdb=" N LEU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 193 removed outlier: 4.229A pdb=" N ASN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 removed outlier: 3.593A 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 228 Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.579A pdb=" N GLN B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 249 removed outlier: 3.589A pdb=" N GLU B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 275 removed outlier: 3.746A pdb=" N LYS B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 380 through 386 removed outlier: 4.148A pdb=" N LEU B 385 " --> pdb=" O GLU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 429 through 440 removed outlier: 3.718A pdb=" N TYR B 433 " --> pdb=" O ARG B 429 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER B 435 " --> pdb=" O ARG B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 471 Processing helix chain 'B' and resid 506 through 515 removed outlier: 3.580A pdb=" N ILE B 510 " --> pdb=" O PRO B 506 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B 515 " --> pdb=" O LYS B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 584 removed outlier: 3.993A 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 614 removed outlier: 5.014A pdb=" N GLU B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TYR B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ALA B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 614 " --> pdb=" O ALA B 610 " (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: 4.102A 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 690 Processing helix chain 'B' and resid 696 through 705 removed outlier: 4.426A pdb=" N ASP B 705 " --> pdb=" O LYS B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 722 removed outlier: 3.651A pdb=" N LEU B 712 " --> pdb=" O THR B 708 " (cutoff:3.500A) Proline residue: B 717 - end of helix removed outlier: 4.398A 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: 3.947A pdb=" N MET B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 823 removed outlier: 3.560A pdb=" N ALA B 819 " --> pdb=" O ILE B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 876 removed outlier: 3.781A pdb=" N GLU B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 894 removed outlier: 3.627A pdb=" N PHE B 882 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 912 Processing helix chain 'B' and resid 919 through 929 Processing helix chain 'B' and resid 932 through 944 removed outlier: 3.512A pdb=" N ILE B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1001 removed outlier: 3.962A 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: 4.073A pdb=" N ARG A 49 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 257 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 87 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 88 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 137 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 360 removed outlier: 4.842A pdb=" N THR A 358 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ARG A 311 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 491 through 492 Processing sheet with id=AA4, first strand: chain 'A' and resid 557 through 558 removed outlier: 6.359A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 557 through 558 removed outlier: 6.359A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS A 724 " --> pdb=" O PHE A 579 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 832 through 840 removed outlier: 4.411A pdb=" N ILE A 832 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 851 " --> pdb=" O ILE A 832 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 840 " --> pdb=" O ILE A 843 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLN A 844 " --> pdb=" O THR A 797 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 63 through 69 removed outlier: 5.981A pdb=" N LYS B 74 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N VAL B 258 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU B 76 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLY B 260 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE B 78 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP B 91 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN B 148 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE B 141 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 304 Processing sheet with id=AA9, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AB1, first strand: chain 'B' and resid 549 through 553 removed outlier: 5.828A pdb=" N LEU B 550 " --> pdb=" O PHE B 561 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE B 561 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 552 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 776 through 777 removed outlier: 6.234A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 776 through 777 removed outlier: 6.234A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B 790 " --> pdb=" O VAL B 958 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 848 " --> pdb=" O ILE B 793 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR B 797 " --> pdb=" O GLN B 844 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN B 844 " --> pdb=" O THR B 797 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE B 832 " --> pdb=" O GLN B 851 " (cutoff:3.500A) 681 hydrogen bonds defined for protein. 1965 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: 5.34 Time building geometry restraints manager: 6.21 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: 3294 1.33 - 1.45: 3585 1.45 - 1.57: 8962 1.57 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 15928 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 1.75e+01 bond pdb=" N VAL B 707 " pdb=" CA VAL B 707 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.19e-02 7.06e+03 1.15e+01 bond pdb=" N VAL B1008 " pdb=" CA VAL B1008 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.49e+00 bond pdb=" N VAL b 2 " pdb=" CA VAL b 2 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.22e-02 6.72e+03 8.89e+00 bond pdb=" N VAL B 585 " pdb=" CA VAL B 585 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.20e-02 6.94e+03 8.79e+00 ... (remaining 15923 not shown) Histogram of bond angle deviations from ideal: 98.18 - 105.40: 403 105.40 - 112.62: 7845 112.62 - 119.84: 6018 119.84 - 127.06: 7098 127.06 - 134.28: 169 Bond angle restraints: 21533 Sorted by residual: angle pdb=" C LEU a 16 " pdb=" CA LEU a 16 " pdb=" CB LEU a 16 " ideal model delta sigma weight residual 116.63 111.17 5.46 1.16e+00 7.43e-01 2.21e+01 angle pdb=" N GLU B 529 " pdb=" CA GLU B 529 " pdb=" C GLU B 529 " ideal model delta sigma weight residual 112.86 107.16 5.70 1.22e+00 6.72e-01 2.18e+01 angle pdb=" CA GLU A 176 " pdb=" CB GLU A 176 " pdb=" CG GLU A 176 " ideal model delta sigma weight residual 114.10 122.46 -8.36 2.00e+00 2.50e-01 1.75e+01 angle pdb=" C ASN B 821 " pdb=" N THR B 822 " pdb=" CA THR B 822 " ideal model delta sigma weight residual 121.52 114.33 7.19 1.84e+00 2.95e-01 1.53e+01 angle pdb=" CA GLY A 775 " pdb=" C GLY A 775 " pdb=" O GLY A 775 " ideal model delta sigma weight residual 121.47 118.04 3.43 9.00e-01 1.23e+00 1.45e+01 ... (remaining 21528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 8764 16.53 - 33.05: 670 33.05 - 49.58: 172 49.58 - 66.10: 25 66.10 - 82.63: 16 Dihedral angle restraints: 9647 sinusoidal: 4049 harmonic: 5598 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 180.00 153.70 26.30 0 5.00e+00 4.00e-02 2.77e+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 -155.22 -24.78 0 5.00e+00 4.00e-02 2.46e+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 180.00 155.37 24.63 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 9644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1482 0.045 - 0.090: 562 0.090 - 0.135: 204 0.135 - 0.180: 49 0.180 - 0.225: 19 Chirality restraints: 2316 Sorted by residual: chirality pdb=" CA TRP A 695 " pdb=" N TRP A 695 " pdb=" C TRP A 695 " pdb=" CB TRP A 695 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA GLN B 770 " pdb=" N GLN B 770 " pdb=" C GLN B 770 " pdb=" CB GLN B 770 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA LYS B 364 " pdb=" N LYS B 364 " pdb=" C LYS B 364 " pdb=" CB LYS B 364 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2313 not shown) Planarity restraints: 2785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 224 " 0.025 2.00e-02 2.50e+03 5.01e-02 2.51e+01 pdb=" C TYR B 224 " -0.087 2.00e-02 2.50e+03 pdb=" O TYR B 224 " 0.032 2.00e-02 2.50e+03 pdb=" N THR B 225 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 822 " -0.023 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C THR B 822 " 0.078 2.00e-02 2.50e+03 pdb=" O THR B 822 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU B 823 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 288 " -0.067 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 289 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 289 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 289 " -0.055 5.00e-02 4.00e+02 ... (remaining 2782 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 211 2.66 - 3.22: 14343 3.22 - 3.78: 22935 3.78 - 4.34: 32482 4.34 - 4.90: 52838 Nonbonded interactions: 122809 Sorted by model distance: nonbonded pdb=" O THR A 83 " pdb=" NH1 ARG A 261 " model vdw 2.098 2.520 nonbonded pdb=" OG SER B 128 " pdb=" OE2 GLU B 817 " model vdw 2.173 2.440 nonbonded pdb=" OG SER A 87 " pdb=" O PHE A 151 " model vdw 2.177 2.440 nonbonded pdb=" OD2 ASP B 91 " pdb=" NE2 HIS B 442 " model vdw 2.187 2.520 nonbonded pdb=" O ARG A 668 " pdb=" ND2 ASN A 672 " model vdw 2.200 2.520 ... (remaining 122804 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 198 or resid 200 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.140 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 40.800 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.005 0.051 15928 Z= 0.339 Angle : 0.967 11.255 21533 Z= 0.593 Chirality : 0.057 0.225 2316 Planarity : 0.008 0.103 2785 Dihedral : 13.090 82.627 6027 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.30 % 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: -3.81 (0.16), residues: 1884 helix: -2.70 (0.14), residues: 766 sheet: -1.98 (0.27), residues: 323 loop : -2.40 (0.19), residues: 795 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 265 time to evaluate : 1.703 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 270 average time/residue: 0.2830 time to fit residues: 114.0263 Evaluate side-chains 173 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 1.847 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1351 time to fit residues: 3.1041 ------------------------------------------------------------------------------- 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: 3.9990 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN A 821 ASN A 914 GLN A 988 GLN B 146 HIS ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN B 762 GLN ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 15928 Z= 0.271 Angle : 0.681 8.841 21533 Z= 0.355 Chirality : 0.047 0.181 2316 Planarity : 0.005 0.063 2785 Dihedral : 5.211 18.178 2060 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 2.07 % 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: -2.09 (0.18), residues: 1884 helix: -0.78 (0.17), residues: 798 sheet: -1.40 (0.26), residues: 338 loop : -1.90 (0.20), residues: 748 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 203 time to evaluate : 1.779 Fit side-chains outliers start: 35 outliers final: 24 residues processed: 227 average time/residue: 0.2657 time to fit residues: 92.6311 Evaluate side-chains 195 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 1.777 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1522 time to fit residues: 9.5074 ------------------------------------------------------------------------------- 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: 2.9990 chunk 52 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 190 HIS ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN A 805 ASN A 821 ASN A 828 GLN B 190 HIS B 291 HIS ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN B 718 GLN B 724 HIS ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.056 15928 Z= 0.475 Angle : 0.811 9.844 21533 Z= 0.419 Chirality : 0.052 0.179 2316 Planarity : 0.006 0.063 2785 Dihedral : 5.520 22.410 2060 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer Outliers : 2.84 % 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: -1.77 (0.18), residues: 1884 helix: -0.40 (0.17), residues: 809 sheet: -1.09 (0.26), residues: 354 loop : -2.00 (0.20), residues: 721 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 171 time to evaluate : 1.699 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 17 residues processed: 210 average time/residue: 0.2668 time to fit residues: 86.3928 Evaluate side-chains 168 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 1.872 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1537 time to fit residues: 7.3680 ------------------------------------------------------------------------------- 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: 0.8980 chunk 128 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 821 ASN ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 15928 Z= 0.177 Angle : 0.567 8.444 21533 Z= 0.293 Chirality : 0.043 0.205 2316 Planarity : 0.004 0.053 2785 Dihedral : 4.817 17.825 2060 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 1.83 % 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: -0.96 (0.19), residues: 1884 helix: 0.30 (0.18), residues: 814 sheet: -0.57 (0.26), residues: 348 loop : -1.69 (0.21), residues: 722 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 186 time to evaluate : 1.950 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 12 residues processed: 210 average time/residue: 0.2650 time to fit residues: 85.5099 Evaluate side-chains 177 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 1.651 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1685 time to fit residues: 5.9567 ------------------------------------------------------------------------------- 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: 2.9990 chunk 103 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 788 ASN A 821 ASN ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 15928 Z= 0.245 Angle : 0.589 7.480 21533 Z= 0.302 Chirality : 0.044 0.199 2316 Planarity : 0.004 0.044 2785 Dihedral : 4.754 18.269 2060 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 1.71 % 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: -0.75 (0.19), residues: 1884 helix: 0.58 (0.18), residues: 816 sheet: -0.52 (0.26), residues: 355 loop : -1.71 (0.21), residues: 713 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 1.821 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 191 average time/residue: 0.2491 time to fit residues: 75.0633 Evaluate side-chains 184 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 170 time to evaluate : 1.853 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1476 time to fit residues: 6.4716 ------------------------------------------------------------------------------- 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: 0.9980 chunk 163 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 821 ASN B 146 HIS ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 828 GLN ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 15928 Z= 0.146 Angle : 0.527 7.200 21533 Z= 0.270 Chirality : 0.042 0.170 2316 Planarity : 0.004 0.040 2785 Dihedral : 4.442 16.853 2060 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 1.18 % 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: -0.35 (0.19), residues: 1884 helix: 0.98 (0.19), residues: 808 sheet: -0.37 (0.27), residues: 344 loop : -1.52 (0.21), residues: 732 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 181 time to evaluate : 1.770 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 193 average time/residue: 0.2602 time to fit residues: 77.8822 Evaluate side-chains 179 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 169 time to evaluate : 1.875 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1627 time to fit residues: 5.4393 ------------------------------------------------------------------------------- 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: 0.0970 chunk 20 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 83 optimal weight: 0.5980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 HIS A 638 GLN ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 15928 Z= 0.284 Angle : 0.616 9.563 21533 Z= 0.313 Chirality : 0.045 0.195 2316 Planarity : 0.004 0.040 2785 Dihedral : 4.672 18.419 2060 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 1.12 % 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: -0.38 (0.19), residues: 1884 helix: 0.93 (0.19), residues: 809 sheet: -0.28 (0.27), residues: 353 loop : -1.56 (0.21), residues: 722 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.855 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 187 average time/residue: 0.2768 time to fit residues: 80.4048 Evaluate side-chains 173 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 2.057 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1560 time to fit residues: 6.1485 ------------------------------------------------------------------------------- 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: 7.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 0.0970 chunk 142 optimal weight: 0.4980 chunk 164 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN B 475 ASN ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 15928 Z= 0.238 Angle : 0.586 8.934 21533 Z= 0.298 Chirality : 0.044 0.172 2316 Planarity : 0.004 0.051 2785 Dihedral : 4.641 17.988 2060 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.89 % 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: -0.29 (0.19), residues: 1884 helix: 1.00 (0.19), residues: 807 sheet: -0.21 (0.27), residues: 351 loop : -1.52 (0.21), residues: 726 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 173 time to evaluate : 1.842 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 182 average time/residue: 0.2772 time to fit residues: 78.2830 Evaluate side-chains 169 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 162 time to evaluate : 1.818 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1512 time to fit residues: 4.8101 ------------------------------------------------------------------------------- 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: 2.9990 chunk 158 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 132 optimal weight: 0.0370 chunk 51 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 overall best weight: 1.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN B 291 HIS ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 15928 Z= 0.225 Angle : 0.576 8.039 21533 Z= 0.293 Chirality : 0.043 0.167 2316 Planarity : 0.004 0.037 2785 Dihedral : 4.608 19.469 2060 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.59 % 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: -0.20 (0.19), residues: 1884 helix: 1.05 (0.19), residues: 808 sheet: -0.17 (0.26), residues: 352 loop : -1.46 (0.22), residues: 724 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 1.835 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 168 average time/residue: 0.2585 time to fit residues: 68.4296 Evaluate side-chains 160 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 1.792 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1496 time to fit residues: 3.5893 ------------------------------------------------------------------------------- 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: 8.9990 chunk 84 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN B 291 HIS B 407 GLN ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 680 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 15928 Z= 0.221 Angle : 0.574 7.966 21533 Z= 0.291 Chirality : 0.043 0.165 2316 Planarity : 0.004 0.037 2785 Dihedral : 4.598 20.942 2060 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 0.59 % 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: -0.14 (0.19), residues: 1884 helix: 1.08 (0.19), residues: 808 sheet: -0.12 (0.26), residues: 352 loop : -1.41 (0.22), residues: 724 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 1.944 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 166 average time/residue: 0.2762 time to fit residues: 71.7413 Evaluate side-chains 165 residues out of total 1693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 1.893 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1647 time to fit residues: 4.2393 ------------------------------------------------------------------------------- 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: 6.9990 chunk 137 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 0.3980 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 18 optimal weight: 0.0470 chunk 27 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 800 GLN A 821 ASN B 291 HIS ** B 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN B 680 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.161756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.137285 restraints weight = 20391.275| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.64 r_work: 0.3442 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 15928 Z= 0.202 Angle : 0.562 8.105 21533 Z= 0.285 Chirality : 0.043 0.158 2316 Planarity : 0.004 0.037 2785 Dihedral : 4.536 20.608 2060 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.53 % 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: -0.04 (0.19), residues: 1884 helix: 1.15 (0.19), residues: 808 sheet: -0.05 (0.27), residues: 352 loop : -1.35 (0.22), residues: 724 =============================================================================== Job complete usr+sys time: 3026.11 seconds wall clock time: 55 minutes 55.99 seconds (3355.99 seconds total)