Starting phenix.real_space_refine on Sat Mar 16 21:17:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzi_24761/03_2024/7rzi_24761.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzi_24761/03_2024/7rzi_24761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzi_24761/03_2024/7rzi_24761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzi_24761/03_2024/7rzi_24761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzi_24761/03_2024/7rzi_24761.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzi_24761/03_2024/7rzi_24761.pdb" } resolution = 3.0 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= 0.009 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 49 5.16 5 C 10134 2.51 5 N 2640 2.21 5 O 2913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A GLU 577": "OE1" <-> "OE2" Residue "A PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 782": "NH1" <-> "NH2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A ARG 862": "NH1" <-> "NH2" Residue "A ARG 892": "NH1" <-> "NH2" Residue "A GLU 910": "OE1" <-> "OE2" Residue "A PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B GLU 277": "OE1" <-> "OE2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B GLU 448": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 660": "OE1" <-> "OE2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B GLU 692": "OE1" <-> "OE2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B GLU 784": "OE1" <-> "OE2" Residue "B GLU 853": "OE1" <-> "OE2" Residue "B ARG 862": "NH1" <-> "NH2" Residue "B ARG 892": "NH1" <-> "NH2" Residue "c GLU 17": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15736 Number of models: 1 Model: "" Number of chains: 6 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: 7692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7692 Classifications: {'peptide': 938} Link IDs: {'PTRANS': 48, 'TRANS': 889} Chain breaks: 1 Chain: "a" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 83 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "b" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "c" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 108 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "d" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Time building chain proxies: 8.60, per 1000 atoms: 0.55 Number of scatterers: 15736 At special positions: 0 Unit cell: (108.42, 131.188, 149.62, 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 49 16.00 O 2913 8.00 N 2640 7.00 C 10134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS a 6 " - pdb=" SG CYS a 11 " distance=1.74 Simple disulfide: pdb=" SG CYS c 6 " - pdb=" SG CYS c 11 " distance=2.05 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: 5.28 Conformation dependent library (CDL) restraints added in 2.3 seconds 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3666 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 10 sheets defined 45.0% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.571A pdb=" N SER A 98 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 3.818A 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: 4.164A 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: 4.298A pdb=" N ARG A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 193 removed outlier: 4.275A pdb=" N VAL A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 removed outlier: 3.627A pdb=" N LEU A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.840A 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 276 Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.545A 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: 3.645A pdb=" N LEU A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 405 removed outlier: 3.701A pdb=" N GLU A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.689A pdb=" N PHE A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 440 removed outlier: 3.520A pdb=" N TYR A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER A 435 " --> pdb=" O ARG A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.863A pdb=" N ILE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 removed outlier: 3.982A pdb=" N ILE A 510 " --> pdb=" O PRO A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 615 removed outlier: 3.821A pdb=" N ALA A 593 " --> pdb=" O HIS A 589 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TYR A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ALA A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA A 611 " --> pdb=" O TYR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 removed outlier: 3.589A pdb=" N LEU A 641 " --> pdb=" O LYS A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.826A pdb=" N GLU A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 3.549A 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: 3.861A pdb=" N ARG A 687 " --> pdb=" O MET A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 removed outlier: 3.787A pdb=" N LEU A 700 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.778A 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 720 removed outlier: 3.538A pdb=" N ILE A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) 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: 3.684A pdb=" N LEU A 763 " --> pdb=" O PRO A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 3.942A pdb=" N LEU A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 824 removed outlier: 3.884A pdb=" N PHE A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 877 removed outlier: 3.516A pdb=" N LEU A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 877 " --> pdb=" O SER A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 894 Processing helix chain 'A' and resid 900 through 912 removed outlier: 3.757A pdb=" N LYS A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 4.130A 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: 3.892A pdb=" N ILE A 936 " --> pdb=" O THR A 932 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1001 removed outlier: 4.116A pdb=" N GLY A1001 " --> pdb=" O GLU A 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 removed outlier: 4.241A pdb=" N PHE B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 removed outlier: 3.697A pdb=" N GLU B 133 " --> pdb=" O GLN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 166 removed outlier: 4.301A pdb=" N ASP B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.885A pdb=" N SER B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 Processing helix chain 'B' and resid 181 through 192 removed outlier: 3.593A pdb=" N ALA B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 207 removed outlier: 3.831A pdb=" N PHE B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 264 through 276 removed outlier: 3.511A pdb=" N THR B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN B 269 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU B 270 " --> pdb=" O ASP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 removed outlier: 3.541A pdb=" N TYR B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 removed outlier: 3.660A pdb=" N LYS B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 408 through 424 removed outlier: 3.533A pdb=" N ASN B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 440 removed outlier: 3.529A pdb=" N THR B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N SER B 435 " --> pdb=" O ARG B 431 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 437 " --> pdb=" O TYR B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 443 No H-bonds generated for 'chain 'B' and resid 441 through 443' Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.767A pdb=" N ILE B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.748A pdb=" N VAL B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 486 Processing helix chain 'B' and resid 506 through 514 removed outlier: 3.589A pdb=" N ILE B 510 " --> pdb=" O PRO B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 604 through 613 removed outlier: 5.087A pdb=" N ALA B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 613 " --> pdb=" O TYR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 650 removed outlier: 3.590A pdb=" N LEU B 641 " --> pdb=" O LYS B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 677 through 691 removed outlier: 3.622A pdb=" N HIS B 681 " --> pdb=" O GLN B 677 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B 682 " --> pdb=" O PRO B 678 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET B 683 " --> pdb=" O HIS B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 704 Processing helix chain 'B' and resid 708 through 714 removed outlier: 3.786A pdb=" N ALA B 714 " --> pdb=" O PRO B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 720 removed outlier: 3.507A pdb=" N GLN B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 754 removed outlier: 3.796A pdb=" N LEU B 739 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 745 " --> pdb=" O ILE B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.659A pdb=" N LEU B 763 " --> pdb=" O PRO B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 815 removed outlier: 3.674A pdb=" N MET B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 807 " --> pdb=" O SER B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 855 through 876 removed outlier: 4.170A pdb=" N SER B 861 " --> pdb=" O HIS B 857 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 862 " --> pdb=" O TYR B 858 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 863 " --> pdb=" O LEU B 859 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU B 875 " --> pdb=" O GLU B 871 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP B 876 " --> pdb=" O LYS B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 893 removed outlier: 3.714A pdb=" N LEU B 889 " --> pdb=" O HIS B 885 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA B 890 " --> pdb=" O ILE B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 912 removed outlier: 3.590A pdb=" N GLU B 903 " --> pdb=" O LYS B 899 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY B 909 " --> pdb=" O ALA B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 929 removed outlier: 3.538A pdb=" N THR B 923 " --> pdb=" O ASP B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 944 removed outlier: 3.575A pdb=" N ILE B 936 " --> pdb=" O THR B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1001 removed outlier: 4.003A 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: 6.016A pdb=" N LYS A 74 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL A 258 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 76 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N GLY A 260 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE A 78 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 88 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 142 " --> pdb=" O SER a 12 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER a 12 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 360 removed outlier: 4.878A pdb=" N THR A 358 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 5.414A 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: 6.416A pdb=" N LYS A 558 " --> pdb=" O ALA A 727 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU A 729 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 724 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 728 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN A 575 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 563 Processing sheet with id=AA6, first strand: chain 'A' and resid 832 through 840 removed outlier: 4.540A pdb=" N ILE A 832 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 851 " --> pdb=" O ILE A 832 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLN A 844 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N HIS A 952 " --> pdb=" O GLN A 796 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TRP A 776 " --> pdb=" O GLU A 990 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.646A pdb=" N GLU B 63 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS B 74 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL B 258 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B 76 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLY B 260 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE B 78 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 88 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 141 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 356 through 367 removed outlier: 4.594A pdb=" N THR B 358 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 366 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLN B 499 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 549 through 553 removed outlier: 6.331A pdb=" N LEU B 550 " --> pdb=" O PHE B 561 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE B 561 " --> pdb=" O LEU B 550 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS B 552 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS B 558 " --> pdb=" O ALA B 727 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU B 729 " --> pdb=" O LYS B 558 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N TRP B 560 " --> pdb=" O LEU B 729 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 775 through 782 removed outlier: 5.918A pdb=" N GLY B 775 " --> pdb=" O LYS B 953 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER B 955 " --> pdb=" O GLY B 775 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE B 777 " --> pdb=" O SER B 955 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N HIS B 957 " --> pdb=" O PHE B 777 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR B 779 " --> pdb=" O HIS B 957 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU B 959 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLN B 781 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU B 792 " --> pdb=" O VAL B 956 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 850 " --> pdb=" O ILE B 791 " (cutoff:3.500A) 661 hydrogen bonds defined for protein. 1902 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: 5.41 Time building geometry restraints manager: 5.78 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: 3459 1.33 - 1.45: 3547 1.45 - 1.57: 9025 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 16123 Sorted by residual: bond pdb=" N GLY B 366 " pdb=" CA GLY B 366 " ideal model delta sigma weight residual 1.447 1.475 -0.028 7.50e-03 1.78e+04 1.41e+01 bond pdb=" N TYR A 766 " pdb=" CA TYR A 766 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.18e-02 7.18e+03 1.04e+01 bond pdb=" N VAL B 360 " pdb=" CA VAL B 360 " ideal model delta sigma weight residual 1.458 1.496 -0.037 1.19e-02 7.06e+03 9.89e+00 bond pdb=" N VAL B 764 " pdb=" CA VAL B 764 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.32e-02 5.74e+03 9.59e+00 bond pdb=" N ILE B 103 " pdb=" CA ILE B 103 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.37e+00 ... (remaining 16118 not shown) Histogram of bond angle deviations from ideal: 95.88 - 103.55: 240 103.55 - 111.22: 6043 111.22 - 118.89: 7005 118.89 - 126.56: 8300 126.56 - 134.23: 209 Bond angle restraints: 21797 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 112.25 105.14 7.11 1.36e+00 5.41e-01 2.73e+01 angle pdb=" N ILE a 10 " pdb=" CA ILE a 10 " pdb=" C ILE a 10 " ideal model delta sigma weight residual 112.90 108.05 4.85 9.60e-01 1.09e+00 2.55e+01 angle pdb=" O GLY B 366 " pdb=" C GLY B 366 " pdb=" N ALA B 367 " ideal model delta sigma weight residual 121.85 124.41 -2.56 5.60e-01 3.19e+00 2.08e+01 angle pdb=" N GLN B 796 " pdb=" CA GLN B 796 " pdb=" C GLN B 796 " ideal model delta sigma weight residual 111.71 116.36 -4.65 1.15e+00 7.56e-01 1.64e+01 angle pdb=" CA GLU A 277 " pdb=" C GLU A 277 " pdb=" O GLU A 277 " ideal model delta sigma weight residual 121.00 116.86 4.14 1.05e+00 9.07e-01 1.56e+01 ... (remaining 21792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 8954 16.92 - 33.83: 654 33.83 - 50.75: 126 50.75 - 67.67: 18 67.67 - 84.58: 11 Dihedral angle restraints: 9763 sinusoidal: 4096 harmonic: 5667 Sorted by residual: dihedral pdb=" CB CYS c 6 " pdb=" SG CYS c 6 " pdb=" SG CYS c 11 " pdb=" CB CYS c 11 " ideal model delta sinusoidal sigma weight residual -86.00 -136.67 50.67 1 1.00e+01 1.00e-02 3.52e+01 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 180.00 153.46 26.54 0 5.00e+00 4.00e-02 2.82e+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 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 9760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1891 0.074 - 0.147: 399 0.147 - 0.221: 46 0.221 - 0.294: 7 0.294 - 0.368: 2 Chirality restraints: 2345 Sorted by residual: chirality pdb=" CA THR B 797 " pdb=" N THR B 797 " pdb=" C THR B 797 " pdb=" CB THR B 797 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA GLN B 796 " pdb=" N GLN B 796 " pdb=" C GLN B 796 " pdb=" CB GLN B 796 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA MET A 742 " pdb=" N MET A 742 " pdb=" C MET A 742 " pdb=" CB MET A 742 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2342 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 821 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C ASN B 821 " 0.069 2.00e-02 2.50e+03 pdb=" O ASN B 821 " -0.026 2.00e-02 2.50e+03 pdb=" N THR B 822 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 224 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C TYR A 224 " -0.063 2.00e-02 2.50e+03 pdb=" O TYR A 224 " 0.024 2.00e-02 2.50e+03 pdb=" N THR A 225 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 223 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C LYS A 223 " 0.056 2.00e-02 2.50e+03 pdb=" O LYS A 223 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR A 224 " -0.019 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1529 2.74 - 3.28: 15138 3.28 - 3.82: 24813 3.82 - 4.36: 31533 4.36 - 4.90: 53395 Nonbonded interactions: 126408 Sorted by model distance: nonbonded pdb=" OG SER A 87 " pdb=" O PHE A 151 " model vdw 2.203 2.440 nonbonded pdb=" NH2 ARG B 402 " pdb=" O LEU B 471 " model vdw 2.209 2.520 nonbonded pdb=" O MET A 877 " pdb=" NZ LYS A 933 " model vdw 2.231 2.520 nonbonded pdb=" OG1 THR A 623 " pdb=" O GLY A 626 " model vdw 2.236 2.440 nonbonded pdb=" O TYR A 634 " pdb=" NE2 GLN A 638 " model vdw 2.248 2.520 ... (remaining 126403 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 990 through 1011)) selection = chain 'B' } ncs_group { reference = chain 'b' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.820 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: 4.660 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 41.270 Find NCS groups from input model: 0.900 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: 0.010 Load rotamer database and sin/cos tables:11.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 : 0.006 0.063 16123 Z= 0.371 Angle : 0.972 10.261 21797 Z= 0.580 Chirality : 0.060 0.368 2345 Planarity : 0.008 0.079 2818 Dihedral : 12.553 84.585 6091 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.47 % Allowed : 2.50 % Favored : 97.03 % Cbeta Deviations : 0.05 % 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: -4.04 (0.15), residues: 1905 helix: -3.20 (0.13), residues: 759 sheet: -1.85 (0.26), residues: 347 loop : -2.32 (0.18), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 695 HIS 0.017 0.002 HIS B 291 PHE 0.042 0.003 PHE A 168 TYR 0.029 0.003 TYR A 940 ARG 0.018 0.001 ARG B 261 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 308 time to evaluate : 1.647 Fit side-chains revert: symmetry clash REVERT: A 195 MET cc_start: 0.8893 (mmt) cc_final: 0.8176 (mmt) REVERT: B 358 THR cc_start: 0.8399 (p) cc_final: 0.8153 (m) REVERT: B 526 THR cc_start: 0.8041 (p) cc_final: 0.7830 (t) REVERT: B 872 LYS cc_start: 0.7825 (mttp) cc_final: 0.7194 (tmmt) REVERT: c 5 GLN cc_start: 0.5489 (OUTLIER) cc_final: 0.4524 (mm110) outliers start: 8 outliers final: 1 residues processed: 314 average time/residue: 1.3809 time to fit residues: 475.9170 Evaluate side-chains 188 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain c residue 5 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 HIS B 93 HIS ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN B 677 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 788 ASN B 796 GLN ** B 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 HIS d 5 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16123 Z= 0.233 Angle : 0.653 8.103 21797 Z= 0.333 Chirality : 0.045 0.167 2345 Planarity : 0.005 0.053 2818 Dihedral : 5.213 23.330 2088 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.44 % Allowed : 10.77 % Favored : 85.79 % 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: -2.26 (0.17), residues: 1905 helix: -1.21 (0.17), residues: 789 sheet: -1.14 (0.26), residues: 363 loop : -1.83 (0.19), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 776 HIS 0.008 0.001 HIS B 957 PHE 0.022 0.002 PHE A 168 TYR 0.023 0.002 TYR B 249 ARG 0.008 0.001 ARG B 477 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 208 time to evaluate : 1.861 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.5733 (m-30) cc_final: 0.5429 (m-30) REVERT: A 146 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.5333 (p90) REVERT: A 175 ASP cc_start: 0.6955 (p0) cc_final: 0.6582 (m-30) REVERT: A 195 MET cc_start: 0.8790 (mmt) cc_final: 0.8166 (mmt) REVERT: A 776 TRP cc_start: 0.7272 (t-100) cc_final: 0.7050 (t-100) REVERT: A 792 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8383 (tm-30) REVERT: B 526 THR cc_start: 0.8177 (p) cc_final: 0.7971 (t) REVERT: B 690 MET cc_start: 0.8328 (mmm) cc_final: 0.8109 (mmp) REVERT: B 774 ARG cc_start: 0.7575 (mtp85) cc_final: 0.7207 (mtp85) REVERT: B 872 LYS cc_start: 0.7839 (mttp) cc_final: 0.7315 (tmmt) outliers start: 59 outliers final: 14 residues processed: 249 average time/residue: 1.3059 time to fit residues: 359.1346 Evaluate side-chains 189 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 173 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 764 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A 680 GLN ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 528 ASN B 671 ASN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 743 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16123 Z= 0.400 Angle : 0.761 9.633 21797 Z= 0.381 Chirality : 0.049 0.164 2345 Planarity : 0.005 0.053 2818 Dihedral : 5.269 23.354 2083 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.89 % Allowed : 12.99 % Favored : 82.12 % 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: -1.57 (0.18), residues: 1905 helix: -0.55 (0.18), residues: 800 sheet: -0.39 (0.27), residues: 358 loop : -1.82 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 776 HIS 0.019 0.002 HIS B 957 PHE 0.030 0.003 PHE B 918 TYR 0.032 0.002 TYR A 302 ARG 0.005 0.001 ARG A 423 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 198 time to evaluate : 1.854 Fit side-chains REVERT: A 146 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.6190 (p90) REVERT: A 448 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: A 483 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8380 (mttt) REVERT: A 543 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6584 (pp20) REVERT: A 621 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.8031 (pm20) REVERT: A 627 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7939 (mtm) REVERT: A 699 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7690 (mt-10) REVERT: A 702 GLU cc_start: 0.7777 (mp0) cc_final: 0.7512 (mp0) REVERT: A 728 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8105 (tt) REVERT: A 787 ASN cc_start: 0.8349 (t0) cc_final: 0.8138 (t0) REVERT: A 792 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8593 (OUTLIER) REVERT: B 188 SER cc_start: 0.8116 (m) cc_final: 0.7381 (p) REVERT: B 205 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6585 (tp30) REVERT: B 321 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7884 (t0) REVERT: B 407 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7808 (tp40) REVERT: B 436 LYS cc_start: 0.7777 (ttpp) cc_final: 0.7438 (mtpp) REVERT: B 730 HIS cc_start: 0.8088 (OUTLIER) cc_final: 0.7214 (p90) REVERT: B 774 ARG cc_start: 0.7609 (mtp85) cc_final: 0.7286 (mtt90) REVERT: B 872 LYS cc_start: 0.7961 (mttp) cc_final: 0.7394 (tmmt) outliers start: 84 outliers final: 34 residues processed: 263 average time/residue: 1.2741 time to fit residues: 372.0824 Evaluate side-chains 226 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 182 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 621 GLN Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 699 GLU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 612 GLU Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 730 HIS Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain a residue 10 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A 635 ASN ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 743 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16123 Z= 0.299 Angle : 0.646 8.012 21797 Z= 0.327 Chirality : 0.046 0.176 2345 Planarity : 0.005 0.051 2818 Dihedral : 4.995 21.818 2083 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 5.18 % Allowed : 15.32 % Favored : 79.50 % 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: -1.05 (0.18), residues: 1905 helix: -0.07 (0.18), residues: 796 sheet: 0.02 (0.28), residues: 362 loop : -1.69 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 776 HIS 0.012 0.002 HIS B 957 PHE 0.023 0.002 PHE B 169 TYR 0.027 0.002 TYR A 302 ARG 0.004 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 197 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: A 146 HIS cc_start: 0.7301 (OUTLIER) cc_final: 0.6129 (p90) REVERT: A 288 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.5362 (p90) REVERT: A 448 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7870 (pt0) REVERT: A 507 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.6558 (p0) REVERT: A 575 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.7897 (p0) REVERT: A 627 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8093 (mtm) REVERT: A 702 GLU cc_start: 0.7892 (mp0) cc_final: 0.7556 (mp0) REVERT: A 728 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.7972 (tt) REVERT: A 792 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8634 (OUTLIER) REVERT: A 924 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8160 (mt-10) REVERT: B 90 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7433 (pt) REVERT: B 123 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7271 (tttm) REVERT: B 159 GLU cc_start: 0.7321 (tp30) cc_final: 0.7099 (tt0) REVERT: B 436 LYS cc_start: 0.7662 (ttpp) cc_final: 0.7357 (mtpp) REVERT: B 667 MET cc_start: 0.7986 (tpp) cc_final: 0.7692 (tpt) REVERT: B 730 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.7232 (p90) REVERT: B 774 ARG cc_start: 0.7549 (mtp85) cc_final: 0.7057 (mtt-85) REVERT: B 872 LYS cc_start: 0.7918 (mttp) cc_final: 0.7406 (tmmt) outliers start: 89 outliers final: 32 residues processed: 260 average time/residue: 1.2504 time to fit residues: 360.0225 Evaluate side-chains 229 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 186 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 HIS Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 249 TYR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 730 HIS Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 956 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 46 optimal weight: 0.3980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A 680 GLN A 787 ASN A 796 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN B 680 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16123 Z= 0.219 Angle : 0.580 7.226 21797 Z= 0.295 Chirality : 0.044 0.144 2345 Planarity : 0.004 0.048 2818 Dihedral : 4.728 21.134 2083 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.07 % Allowed : 16.13 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.19), residues: 1905 helix: 0.33 (0.18), residues: 796 sheet: 0.17 (0.28), residues: 359 loop : -1.55 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 776 HIS 0.007 0.001 HIS B 957 PHE 0.020 0.002 PHE B 169 TYR 0.017 0.001 TYR B 249 ARG 0.005 0.000 ARG A 961 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 196 time to evaluate : 1.917 Fit side-chains revert: symmetry clash REVERT: A 146 HIS cc_start: 0.7171 (OUTLIER) cc_final: 0.6516 (p90) REVERT: A 288 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.5279 (p90) REVERT: A 448 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7831 (pt0) REVERT: A 507 ASP cc_start: 0.6642 (OUTLIER) cc_final: 0.6421 (p0) REVERT: A 543 GLU cc_start: 0.6799 (pp20) cc_final: 0.6522 (pp20) REVERT: A 575 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.7859 (p0) REVERT: A 627 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8092 (mtm) REVERT: A 632 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8269 (ptpp) REVERT: A 792 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8532 (tp30) REVERT: A 871 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7154 (pt0) REVERT: A 924 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8113 (mt-10) REVERT: B 90 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7281 (pt) REVERT: B 205 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6595 (tp30) REVERT: B 436 LYS cc_start: 0.7590 (ttpp) cc_final: 0.7280 (mtpp) REVERT: B 521 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6647 (pttp) REVERT: B 774 ARG cc_start: 0.7545 (mtp85) cc_final: 0.7105 (mtt-85) REVERT: B 872 LYS cc_start: 0.7948 (mttp) cc_final: 0.7384 (tmmt) outliers start: 87 outliers final: 34 residues processed: 261 average time/residue: 1.2766 time to fit residues: 370.6714 Evaluate side-chains 223 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 176 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 507 ASP Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 701 LYS Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 2.9990 chunk 164 optimal weight: 0.0000 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 45 optimal weight: 0.0470 chunk 182 optimal weight: 5.9990 chunk 151 optimal weight: 0.0970 chunk 84 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 overall best weight: 0.3680 ------------------------------------------------------------------------------- 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 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN A 573 ASN A 621 GLN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 ASN A 796 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16123 Z= 0.133 Angle : 0.495 6.199 21797 Z= 0.255 Chirality : 0.041 0.143 2345 Planarity : 0.004 0.043 2818 Dihedral : 4.279 19.755 2083 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.79 % Allowed : 18.05 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 1905 helix: 0.83 (0.19), residues: 799 sheet: 0.17 (0.27), residues: 368 loop : -1.33 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 560 HIS 0.008 0.001 HIS B 155 PHE 0.014 0.001 PHE B 169 TYR 0.014 0.001 TYR B 500 ARG 0.004 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 204 time to evaluate : 1.813 Fit side-chains revert: symmetry clash REVERT: A 146 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.5053 (p90) REVERT: A 205 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: A 288 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.5237 (p90) REVERT: A 448 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7604 (pt0) REVERT: A 543 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6454 (pp20) REVERT: A 575 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.7625 (p0) REVERT: A 632 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7707 (pttm) REVERT: A 728 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7614 (tt) REVERT: A 816 SER cc_start: 0.8513 (t) cc_final: 0.8290 (p) REVERT: B 68 GLU cc_start: 0.5960 (mt-10) cc_final: 0.5739 (mt-10) REVERT: B 436 LYS cc_start: 0.7514 (ttpp) cc_final: 0.7221 (mtpp) REVERT: B 521 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6501 (pttp) REVERT: B 774 ARG cc_start: 0.7467 (mtp85) cc_final: 0.7189 (mtp85) REVERT: B 872 LYS cc_start: 0.7825 (mttp) cc_final: 0.7324 (tmmt) REVERT: B 994 ASN cc_start: 0.7870 (p0) cc_final: 0.7189 (p0) REVERT: B 997 GLU cc_start: 0.7456 (tt0) cc_final: 0.7102 (tt0) outliers start: 65 outliers final: 23 residues processed: 250 average time/residue: 1.2127 time to fit residues: 337.3724 Evaluate side-chains 217 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 102 optimal weight: 0.3980 chunk 182 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN A 621 GLN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN A 796 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 16123 Z= 0.301 Angle : 0.630 7.968 21797 Z= 0.316 Chirality : 0.046 0.148 2345 Planarity : 0.004 0.046 2818 Dihedral : 4.599 19.678 2083 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.66 % Allowed : 18.11 % Favored : 77.23 % 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: -0.24 (0.19), residues: 1905 helix: 0.73 (0.19), residues: 799 sheet: 0.39 (0.28), residues: 364 loop : -1.40 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 776 HIS 0.009 0.001 HIS B 957 PHE 0.025 0.002 PHE A 174 TYR 0.018 0.002 TYR B 500 ARG 0.016 0.001 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 188 time to evaluate : 1.752 Fit side-chains REVERT: A 288 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.6057 (p90) REVERT: A 448 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7737 (pt0) REVERT: A 503 GLU cc_start: 0.4634 (tt0) cc_final: 0.4339 (mm-30) REVERT: A 507 ASP cc_start: 0.6561 (OUTLIER) cc_final: 0.6305 (p0) REVERT: A 575 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.7787 (p0) REVERT: A 632 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8304 (ptpp) REVERT: A 728 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.7945 (tt) REVERT: A 871 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7130 (pt0) REVERT: A 924 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: B 90 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7349 (pt) REVERT: B 137 SER cc_start: 0.8226 (m) cc_final: 0.7978 (p) REVERT: B 163 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.6870 (m-30) REVERT: B 188 SER cc_start: 0.8053 (OUTLIER) cc_final: 0.7340 (p) REVERT: B 205 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6676 (tp30) REVERT: B 436 LYS cc_start: 0.7688 (ttpp) cc_final: 0.7391 (mtpp) REVERT: B 667 MET cc_start: 0.8061 (tpp) cc_final: 0.7786 (tpt) REVERT: B 774 ARG cc_start: 0.7572 (mtp85) cc_final: 0.7082 (mtt-85) REVERT: B 872 LYS cc_start: 0.8017 (mttp) cc_final: 0.7377 (tmmt) REVERT: B 962 GLU cc_start: 0.6574 (mm-30) cc_final: 0.6313 (mm-30) outliers start: 80 outliers final: 30 residues processed: 249 average time/residue: 1.2371 time to fit residues: 341.2506 Evaluate side-chains 218 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 502 GLN Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 1008 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 0.0270 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- 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 621 GLN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16123 Z= 0.319 Angle : 0.641 8.416 21797 Z= 0.323 Chirality : 0.047 0.184 2345 Planarity : 0.004 0.043 2818 Dihedral : 4.710 19.838 2083 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.14 % Allowed : 19.16 % Favored : 76.70 % 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: -0.28 (0.19), residues: 1905 helix: 0.69 (0.18), residues: 797 sheet: 0.43 (0.28), residues: 365 loop : -1.45 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 776 HIS 0.010 0.002 HIS B 957 PHE 0.023 0.002 PHE B 169 TYR 0.018 0.002 TYR B 500 ARG 0.005 0.001 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 179 time to evaluate : 1.752 Fit side-chains REVERT: A 119 LYS cc_start: 0.8358 (ptpp) cc_final: 0.7521 (mmtm) REVERT: A 288 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.6240 (p90) REVERT: A 363 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.6899 (pp30) REVERT: A 460 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7252 (mtm110) REVERT: A 503 GLU cc_start: 0.4917 (tt0) cc_final: 0.4456 (mm-30) REVERT: A 507 ASP cc_start: 0.6568 (OUTLIER) cc_final: 0.6309 (p0) REVERT: A 543 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6724 (pp20) REVERT: A 575 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.7819 (p0) REVERT: A 632 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8320 (ptpp) REVERT: A 657 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7285 (mttp) REVERT: A 728 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.7977 (tt) REVERT: A 871 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7136 (pt0) REVERT: A 924 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: B 90 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7476 (pt) REVERT: B 137 SER cc_start: 0.8398 (m) cc_final: 0.8127 (p) REVERT: B 163 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.6821 (m-30) REVERT: B 205 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6715 (tp30) REVERT: B 436 LYS cc_start: 0.7751 (ttpp) cc_final: 0.7439 (mtpp) REVERT: B 667 MET cc_start: 0.8041 (tpp) cc_final: 0.7762 (tpt) REVERT: B 730 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7190 (p90) REVERT: B 774 ARG cc_start: 0.7582 (mtp85) cc_final: 0.7093 (mtt-85) REVERT: B 872 LYS cc_start: 0.8029 (mttp) cc_final: 0.7398 (tmmt) REVERT: B 962 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6395 (mm-30) outliers start: 71 outliers final: 34 residues processed: 232 average time/residue: 1.3180 time to fit residues: 338.2826 Evaluate side-chains 223 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 174 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 460 ARG Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 921 ASP Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 730 HIS Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 956 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 0.8980 chunk 159 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 179 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 HIS A 621 GLN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 GLN ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16123 Z= 0.179 Angle : 0.541 7.485 21797 Z= 0.276 Chirality : 0.043 0.156 2345 Planarity : 0.004 0.038 2818 Dihedral : 4.429 19.678 2083 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.15 % Allowed : 20.09 % Favored : 76.76 % 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: 0.00 (0.19), residues: 1905 helix: 0.98 (0.19), residues: 801 sheet: 0.43 (0.28), residues: 360 loop : -1.28 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 495 HIS 0.009 0.001 HIS B 155 PHE 0.020 0.001 PHE B 169 TYR 0.015 0.001 TYR B 500 ARG 0.002 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 182 time to evaluate : 1.912 Fit side-chains REVERT: A 91 ASP cc_start: 0.7946 (t0) cc_final: 0.7740 (t70) REVERT: A 146 HIS cc_start: 0.6957 (OUTLIER) cc_final: 0.6384 (p90) REVERT: A 277 GLU cc_start: 0.7281 (tt0) cc_final: 0.7009 (mt-10) REVERT: A 288 PHE cc_start: 0.6300 (OUTLIER) cc_final: 0.5889 (p90) REVERT: A 363 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.6794 (pp30) REVERT: A 507 ASP cc_start: 0.6508 (OUTLIER) cc_final: 0.6257 (p0) REVERT: A 514 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6381 (pt0) REVERT: A 543 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6761 (pp20) REVERT: A 575 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.7771 (p0) REVERT: A 632 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8206 (ptpp) REVERT: A 657 LYS cc_start: 0.7545 (ptpt) cc_final: 0.7242 (mttp) REVERT: A 728 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7763 (tt) REVERT: A 924 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8093 (mt-10) REVERT: B 90 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7103 (pt) REVERT: B 137 SER cc_start: 0.8426 (m) cc_final: 0.8120 (p) REVERT: B 436 LYS cc_start: 0.7643 (ttpp) cc_final: 0.7296 (mtpp) REVERT: B 521 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6651 (pttp) REVERT: B 621 GLN cc_start: 0.8326 (mt0) cc_final: 0.7842 (mp10) REVERT: B 667 MET cc_start: 0.8037 (tpp) cc_final: 0.7774 (tpt) REVERT: B 774 ARG cc_start: 0.7552 (mtp85) cc_final: 0.7084 (mtt-85) REVERT: B 872 LYS cc_start: 0.8023 (mttp) cc_final: 0.7468 (tmmt) REVERT: B 943 MET cc_start: 0.7753 (mmm) cc_final: 0.7300 (mmm) outliers start: 54 outliers final: 26 residues processed: 219 average time/residue: 1.2810 time to fit residues: 310.6522 Evaluate side-chains 216 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 178 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 921 ASP Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 91 optimal weight: 0.0970 chunk 119 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 621 GLN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16123 Z= 0.170 Angle : 0.532 6.838 21797 Z= 0.271 Chirality : 0.042 0.140 2345 Planarity : 0.004 0.036 2818 Dihedral : 4.294 19.118 2083 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.85 % Allowed : 20.56 % Favored : 76.59 % 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: 0.18 (0.19), residues: 1905 helix: 1.13 (0.19), residues: 803 sheet: 0.49 (0.28), residues: 360 loop : -1.18 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 776 HIS 0.010 0.001 HIS B 155 PHE 0.019 0.001 PHE B 169 TYR 0.016 0.001 TYR B 500 ARG 0.002 0.000 ARG A 181 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 184 time to evaluate : 1.615 Fit side-chains REVERT: A 91 ASP cc_start: 0.7948 (t0) cc_final: 0.7734 (t70) REVERT: A 146 HIS cc_start: 0.6818 (OUTLIER) cc_final: 0.6388 (p90) REVERT: A 277 GLU cc_start: 0.7225 (tt0) cc_final: 0.6898 (tt0) REVERT: A 288 PHE cc_start: 0.6366 (OUTLIER) cc_final: 0.5919 (p90) REVERT: A 363 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.6746 (pp30) REVERT: A 507 ASP cc_start: 0.6468 (OUTLIER) cc_final: 0.6237 (p0) REVERT: A 514 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6410 (pt0) REVERT: A 575 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.7710 (p0) REVERT: A 632 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8162 (ptpp) REVERT: A 657 LYS cc_start: 0.7659 (ptpt) cc_final: 0.7281 (mttp) REVERT: A 728 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7690 (tt) REVERT: A 816 SER cc_start: 0.8584 (t) cc_final: 0.8288 (p) REVERT: A 924 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: B 90 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7012 (pt) REVERT: B 137 SER cc_start: 0.8419 (m) cc_final: 0.8124 (p) REVERT: B 436 LYS cc_start: 0.7667 (ttpp) cc_final: 0.7322 (mtpp) REVERT: B 521 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6429 (pttp) REVERT: B 621 GLN cc_start: 0.8201 (mt0) cc_final: 0.7947 (mp10) REVERT: B 667 MET cc_start: 0.8039 (tpp) cc_final: 0.7761 (tpt) REVERT: B 774 ARG cc_start: 0.7548 (mtp85) cc_final: 0.7070 (mtt-85) REVERT: B 872 LYS cc_start: 0.8045 (mttp) cc_final: 0.7464 (tmmt) REVERT: B 943 MET cc_start: 0.7735 (mmm) cc_final: 0.7273 (mmm) outliers start: 49 outliers final: 27 residues processed: 215 average time/residue: 1.2579 time to fit residues: 302.1240 Evaluate side-chains 213 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 514 GLN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ASN Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 921 ASP Chi-restraints excluded: chain A residue 924 GLU Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 248 TYR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 526 THR Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 759 LEU Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 0.0870 chunk 150 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 131 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- 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 332 HIS A 621 GLN A 680 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 ASN ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.145390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.125479 restraints weight = 16805.032| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.14 r_work: 0.3327 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16123 Z= 0.151 Angle : 0.513 6.897 21797 Z= 0.263 Chirality : 0.042 0.140 2345 Planarity : 0.004 0.036 2818 Dihedral : 4.179 18.520 2083 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.33 % Allowed : 20.85 % Favored : 76.82 % 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: 0.36 (0.19), residues: 1905 helix: 1.31 (0.19), residues: 803 sheet: 0.53 (0.28), residues: 360 loop : -1.09 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 560 HIS 0.011 0.001 HIS B 155 PHE 0.017 0.001 PHE B 169 TYR 0.016 0.001 TYR B 500 ARG 0.002 0.000 ARG B 774 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5891.54 seconds wall clock time: 104 minutes 41.26 seconds (6281.26 seconds total)