Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 8 01:04:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzi_24761/10_2023/7rzi_24761.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzi_24761/10_2023/7rzi_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_24761/10_2023/7rzi_24761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzi_24761/10_2023/7rzi_24761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzi_24761/10_2023/7rzi_24761.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rzi_24761/10_2023/7rzi_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-1.21rc1-5097/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: 8.47, per 1000 atoms: 0.54 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: 5.85 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: 1.61 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: 5.38 Time building geometry restraints manager: 6.34 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: 0.010 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.460 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 43.350 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.520 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.856 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 314 average time/residue: 1.3620 time to fit residues: 470.3469 Evaluate side-chains 187 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 1.902 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2245 time to fit residues: 3.1637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 148 ASN ** 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** d 5 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16123 Z= 0.233 Angle : 0.653 7.934 21797 Z= 0.333 Chirality : 0.045 0.160 2345 Planarity : 0.005 0.052 2818 Dihedral : 5.141 23.139 2083 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.73 % Allowed : 10.83 % Favored : 85.44 % 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: -2.23 (0.17), residues: 1905 helix: -1.15 (0.17), residues: 790 sheet: -1.19 (0.26), residues: 368 loop : -1.80 (0.19), residues: 747 *********************** 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 274 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 210 time to evaluate : 1.793 Fit side-chains revert: symmetry clash outliers start: 64 outliers final: 17 residues processed: 253 average time/residue: 1.2605 time to fit residues: 354.1421 Evaluate side-chains 189 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 172 time to evaluate : 1.881 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.1731 time to fit residues: 3.5259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 47 optimal weight: 0.0470 chunk 171 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 0.0970 overall best weight: 0.9880 ------------------------------------------------------------------------------- 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 796 GLN ** A 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 844 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN B 93 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16123 Z= 0.202 Angle : 0.577 6.974 21797 Z= 0.295 Chirality : 0.043 0.155 2345 Planarity : 0.004 0.049 2818 Dihedral : 4.742 22.539 2083 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.96 % Allowed : 14.15 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.18), residues: 1905 helix: -0.15 (0.18), residues: 791 sheet: -0.49 (0.27), residues: 361 loop : -1.65 (0.20), residues: 753 *********************** 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 258 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 190 time to evaluate : 1.706 Fit side-chains outliers start: 68 outliers final: 28 residues processed: 240 average time/residue: 1.2641 time to fit residues: 337.5675 Evaluate side-chains 197 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 169 time to evaluate : 1.634 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 22 residues processed: 6 average time/residue: 0.1712 time to fit residues: 4.1999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 788 ASN ** 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 671 ASN ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16123 Z= 0.304 Angle : 0.647 7.501 21797 Z= 0.326 Chirality : 0.046 0.150 2345 Planarity : 0.004 0.049 2818 Dihedral : 4.832 21.730 2083 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.89 % Allowed : 14.97 % Favored : 80.14 % 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: -0.88 (0.19), residues: 1905 helix: 0.16 (0.18), residues: 793 sheet: -0.11 (0.28), residues: 363 loop : -1.57 (0.20), residues: 749 *********************** 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 279 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 195 time to evaluate : 1.859 Fit side-chains revert: symmetry clash outliers start: 84 outliers final: 33 residues processed: 259 average time/residue: 1.2459 time to fit residues: 360.7800 Evaluate side-chains 206 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.804 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 23 residues processed: 10 average time/residue: 0.7680 time to fit residues: 11.5906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 680 GLN ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 ASN ** 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 605 ASN ** B 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16123 Z= 0.270 Angle : 0.607 7.570 21797 Z= 0.308 Chirality : 0.045 0.144 2345 Planarity : 0.004 0.048 2818 Dihedral : 4.741 21.510 2083 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.78 % Allowed : 17.01 % Favored : 78.22 % 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: -0.59 (0.19), residues: 1905 helix: 0.41 (0.19), residues: 795 sheet: 0.17 (0.28), residues: 365 loop : -1.52 (0.21), residues: 745 *********************** 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 270 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 188 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 37 residues processed: 246 average time/residue: 1.2237 time to fit residues: 337.1084 Evaluate side-chains 211 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 1.838 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 28 residues processed: 9 average time/residue: 0.5631 time to fit residues: 8.7565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 107 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16123 Z= 0.173 Angle : 0.530 6.428 21797 Z= 0.271 Chirality : 0.042 0.138 2345 Planarity : 0.004 0.043 2818 Dihedral : 4.437 20.906 2083 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.96 % Allowed : 18.46 % Favored : 77.58 % 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: 0.79 (0.19), residues: 797 sheet: 0.28 (0.28), residues: 363 loop : -1.33 (0.21), residues: 745 *********************** 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 252 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 184 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 29 residues processed: 237 average time/residue: 1.3165 time to fit residues: 348.9854 Evaluate side-chains 203 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 174 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 4 average time/residue: 0.2327 time to fit residues: 3.9922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 0.0270 chunk 20 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 182 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS A 502 GLN ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7909 moved from start: 0.3715 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= 0.194 Angle : 0.547 11.230 21797 Z= 0.276 Chirality : 0.043 0.138 2345 Planarity : 0.004 0.043 2818 Dihedral : 4.374 20.249 2083 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.79 % Allowed : 19.28 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.19), residues: 1905 helix: 0.93 (0.19), residues: 799 sheet: 0.40 (0.28), residues: 364 loop : -1.28 (0.21), residues: 742 *********************** 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 251 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 186 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 31 residues processed: 232 average time/residue: 1.2613 time to fit residues: 326.6231 Evaluate side-chains 210 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 179 time to evaluate : 1.799 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 24 residues processed: 7 average time/residue: 0.2262 time to fit residues: 5.0298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 0.0020 chunk 72 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 143 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.6192 ------------------------------------------------------------------------------- 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 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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: 0.7956 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16123 Z= 0.274 Angle : 0.609 7.462 21797 Z= 0.307 Chirality : 0.045 0.146 2345 Planarity : 0.004 0.044 2818 Dihedral : 4.563 20.070 2083 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.15 % Allowed : 19.92 % Favored : 76.94 % 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: -0.09 (0.19), residues: 1905 helix: 0.87 (0.19), residues: 799 sheet: 0.43 (0.28), residues: 365 loop : -1.31 (0.21), residues: 741 *********************** 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 230 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 176 time to evaluate : 1.844 Fit side-chains revert: symmetry clash outliers start: 54 outliers final: 33 residues processed: 219 average time/residue: 1.3335 time to fit residues: 324.8623 Evaluate side-chains 202 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 169 time to evaluate : 1.967 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 27 residues processed: 7 average time/residue: 0.4671 time to fit residues: 6.8461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 0.0060 chunk 159 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 chunk 179 optimal weight: 0.7980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN A 621 GLN ** A 680 GLN ** 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** ** 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 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 732 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3890 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= 0.162 Angle : 0.528 7.319 21797 Z= 0.270 Chirality : 0.042 0.141 2345 Planarity : 0.004 0.041 2818 Dihedral : 4.320 19.785 2083 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.56 % Allowed : 20.50 % Favored : 76.94 % 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: 0.16 (0.19), residues: 1905 helix: 1.10 (0.19), residues: 802 sheet: 0.46 (0.28), residues: 364 loop : -1.16 (0.22), residues: 739 *********************** 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 222 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 178 time to evaluate : 1.935 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 31 residues processed: 214 average time/residue: 1.2856 time to fit residues: 306.5821 Evaluate side-chains 203 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 1.690 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 28 residues processed: 5 average time/residue: 0.4008 time to fit residues: 5.0991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 124 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** A 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS A 621 GLN ** A 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN A 805 ASN A 844 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16123 Z= 0.377 Angle : 0.701 8.710 21797 Z= 0.351 Chirality : 0.048 0.219 2345 Planarity : 0.005 0.044 2818 Dihedral : 4.776 19.944 2083 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.68 % Allowed : 20.44 % Favored : 76.88 % 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: -0.23 (0.19), residues: 1905 helix: 0.69 (0.18), residues: 805 sheet: 0.41 (0.28), residues: 370 loop : -1.38 (0.22), residues: 730 ********************** 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 220 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 174 time to evaluate : 1.933 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 30 residues processed: 212 average time/residue: 1.3266 time to fit residues: 313.1238 Evaluate side-chains 200 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 170 time to evaluate : 1.990 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 27 residues processed: 5 average time/residue: 0.2649 time to fit residues: 4.7404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 131 optimal weight: 0.0770 chunk 8 optimal weight: 4.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 HIS A 621 GLN ** A 680 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** ** c 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.124102 restraints weight = 16823.744| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.16 r_work: 0.3287 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16123 Z= 0.175 Angle : 0.548 6.934 21797 Z= 0.280 Chirality : 0.043 0.158 2345 Planarity : 0.004 0.039 2818 Dihedral : 4.432 18.868 2083 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.98 % Allowed : 21.55 % Favored : 76.47 % 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: 0.10 (0.19), residues: 1905 helix: 1.06 (0.19), residues: 799 sheet: 0.39 (0.28), residues: 365 loop : -1.17 (0.22), residues: 741 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5825.26 seconds wall clock time: 103 minutes 57.90 seconds (6237.90 seconds total)