Starting phenix.real_space_refine on Tue Mar 19 14:20:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfi_33791/03_2024/7yfi_33791_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfi_33791/03_2024/7yfi_33791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfi_33791/03_2024/7yfi_33791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfi_33791/03_2024/7yfi_33791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfi_33791/03_2024/7yfi_33791_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfi_33791/03_2024/7yfi_33791_neut.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 15374 2.51 5 N 4066 2.21 5 O 4567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 39": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C GLU 662": "OE1" <-> "OE2" Residue "C ARG 663": "NH1" <-> "NH2" Residue "C TYR 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 751": "OE1" <-> "OE2" Residue "C GLU 781": "OE1" <-> "OE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "B GLU 906": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24135 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 5941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5941 Classifications: {'peptide': 748} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 714} Chain breaks: 2 Chain: "B" Number of atoms: 5805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5805 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 27, 'TRANS': 706} Chain breaks: 2 Chain: "C" Number of atoms: 5920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5920 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 711} Chain breaks: 2 Chain: "D" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5815 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 39, 'TRANS': 709} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 103 Unusual residues: {'NAG': 7} Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 80 Unusual residues: {'NAG': 5} Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 103 Unusual residues: {'NAG': 7} Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.58, per 1000 atoms: 0.52 Number of scatterers: 24135 At special positions: 0 Unit cell: (155.295, 180.999, 125.307, 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 128 16.00 O 4567 8.00 N 4066 7.00 C 15374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS B 745 " - pdb=" SG CYS B 800 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 317 " distance=2.03 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 453 " distance=2.03 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " distance=2.04 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=1, symmetry=0 Links applied ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG O 2 " - " MAN O 3 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 801 " - " ASN A 203 " " NAG A 802 " - " ASN A 239 " " NAG A 803 " - " ASN A 276 " " NAG A 804 " - " ASN A 300 " " NAG A 805 " - " ASN A 350 " " NAG A 806 " - " ASN A 440 " " NAG A 807 " - " ASN A 491 " " NAG B 901 " - " ASN B 75 " " NAG B 902 " - " ASN B 340 " " NAG B 903 " - " ASN B 380 " " NAG B 904 " - " ASN B 444 " " NAG B 905 " - " ASN B 443 " " NAG C 801 " - " ASN C 239 " " NAG C 802 " - " ASN C 300 " " NAG C 803 " - " ASN C 368 " " NAG C 804 " - " ASN C 350 " " NAG C 805 " - " ASN C 440 " " NAG C 806 " - " ASN C 491 " " NAG C 807 " - " ASN C 771 " " NAG D 901 " - " ASN D 70 " " NAG D 902 " - " ASN D 438 " " NAG E 1 " - " ASN A 61 " " NAG F 1 " - " ASN A 368 " " NAG G 1 " - " ASN A 471 " " NAG H 1 " - " ASN A 771 " " NAG I 1 " - " ASN B 687 " " NAG J 1 " - " ASN C 276 " " NAG K 1 " - " ASN C 61 " " NAG L 1 " - " ASN C 203 " " NAG M 1 " - " ASN C 471 " " NAG N 1 " - " ASN D 337 " " NAG O 1 " - " ASN D 685 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.37 Conformation dependent library (CDL) restraints added in 3.7 seconds 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5556 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 32 sheets defined 42.2% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 35 through 52 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.996A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.642A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.890A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 188 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.894A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.744A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.817A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 297 Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 550 through 556 removed outlier: 4.104A pdb=" N SER A 553 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 584 Processing helix chain 'A' and resid 603 through 613 Processing helix chain 'A' and resid 628 through 655 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.548A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 708 removed outlier: 4.026A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.955A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.735A pdb=" N VAL B 46 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.734A pdb=" N LEU B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.744A pdb=" N GLN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 116 " --> pdb=" O MET B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 213 through 221 removed outlier: 4.526A pdb=" N VAL B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 247 Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 287 through 310 removed outlier: 3.538A pdb=" N LYS B 309 " --> pdb=" O SER B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 472 Processing helix chain 'B' and resid 495 through 502 Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'B' and resid 603 through 613 removed outlier: 3.876A pdb=" N LEU B 607 " --> pdb=" O LYS B 603 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE B 613 " --> pdb=" O TRP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 655 Processing helix chain 'B' and resid 667 through 672 Processing helix chain 'B' and resid 673 through 676 Processing helix chain 'B' and resid 688 through 698 Processing helix chain 'B' and resid 698 through 706 Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 732 through 742 Processing helix chain 'B' and resid 770 through 785 removed outlier: 4.730A pdb=" N GLN B 774 " --> pdb=" O PRO B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 796 Processing helix chain 'B' and resid 814 through 834 Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 104 through 114 removed outlier: 4.175A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.527A pdb=" N SER C 129 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 158 removed outlier: 4.052A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.635A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 251 through 260 removed outlier: 6.574A pdb=" N GLY C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASN C 257 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 297 removed outlier: 3.795A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 457 through 470 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 551 through 556 Processing helix chain 'C' and resid 561 through 584 Processing helix chain 'C' and resid 606 through 613 Processing helix chain 'C' and resid 628 through 658 removed outlier: 3.507A pdb=" N ASP C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.660A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 708 removed outlier: 4.167A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 768 through 782 removed outlier: 3.632A pdb=" N VAL C 772 " --> pdb=" O TRP C 768 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'D' and resid 73 through 86 Processing helix chain 'D' and resid 102 through 116 removed outlier: 4.376A pdb=" N GLN D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 145 through 160 removed outlier: 3.568A pdb=" N GLN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 189 Processing helix chain 'D' and resid 203 through 207 removed outlier: 3.704A pdb=" N GLY D 206 " --> pdb=" O LEU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 217 Processing helix chain 'D' and resid 229 through 244 Processing helix chain 'D' and resid 255 through 260 removed outlier: 3.797A pdb=" N LEU D 259 " --> pdb=" O PRO D 255 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY D 260 " --> pdb=" O ASN D 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 260' Processing helix chain 'D' and resid 284 through 307 Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 456 through 470 Processing helix chain 'D' and resid 493 through 500 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 601 through 611 removed outlier: 4.221A pdb=" N LEU D 605 " --> pdb=" O LYS D 601 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE D 611 " --> pdb=" O TRP D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 653 Processing helix chain 'D' and resid 665 through 670 removed outlier: 3.510A pdb=" N GLN D 669 " --> pdb=" O ASP D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 696 through 705 removed outlier: 4.358A pdb=" N LYS D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 721 Processing helix chain 'D' and resid 730 through 739 Processing helix chain 'D' and resid 768 through 783 removed outlier: 4.724A pdb=" N ALA D 772 " --> pdb=" O HIS D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 793 Processing helix chain 'D' and resid 811 through 835 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 7.990A pdb=" N VAL A 87 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 196 removed outlier: 3.846A pdb=" N LYS A 193 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 270 removed outlier: 6.751A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 478 removed outlier: 5.353A pdb=" N ALA A 515 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLY A 759 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU A 517 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLY A 757 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N PHE A 754 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 538 " --> pdb=" O PHE A 754 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 528 through 529 removed outlier: 5.810A pdb=" N PHE A 754 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 538 " --> pdb=" O PHE A 754 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 487 through 490 removed outlier: 3.874A pdb=" N LYS A 495 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 73 removed outlier: 6.522A pdb=" N ILE B 36 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU B 72 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 38 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 98 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.744A pdb=" N PHE B 170 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASN B 202 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 172 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL B 363 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 342 through 343 Processing sheet with id=AB2, first strand: chain 'B' and resid 474 through 479 removed outlier: 3.895A pdb=" N ILE B 408 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B 507 " --> pdb=" O SER B 407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AB4, first strand: chain 'B' and resid 486 through 489 Processing sheet with id=AB5, first strand: chain 'B' and resid 529 through 531 removed outlier: 4.196A pdb=" N VAL B 529 " --> pdb=" O TYR B 761 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 759 " --> pdb=" O THR B 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 682 through 683 removed outlier: 6.281A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N ASP B 731 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 59 through 66 removed outlier: 6.267A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR C 63 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE C 29 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 193 through 197 removed outlier: 7.061A pdb=" N ILE C 163 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LEU C 195 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.370A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 339 through 340 removed outlier: 4.269A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 474 through 478 removed outlier: 6.876A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 514 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU C 517 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY C 757 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG C 755 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLN C 536 " --> pdb=" O ARG C 755 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY C 757 " --> pdb=" O LYS C 534 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS C 534 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 528 through 529 removed outlier: 5.080A pdb=" N ARG C 755 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLN C 536 " --> pdb=" O ARG C 755 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY C 757 " --> pdb=" O LYS C 534 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS C 534 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC5, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AC6, first strand: chain 'D' and resid 62 through 68 removed outlier: 3.639A pdb=" N GLY D 92 " --> pdb=" O THR D 31 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE D 119 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 194 through 195 removed outlier: 9.045A pdb=" N LEU D 199 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 167 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU D 201 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR D 169 " --> pdb=" O LEU D 201 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 194 through 195 removed outlier: 4.038A pdb=" N VAL D 223 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 274 through 278 removed outlier: 6.693A pdb=" N MET D 358 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG D 374 " --> pdb=" O MET D 358 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL D 360 " --> pdb=" O VAL D 372 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AD2, first strand: chain 'D' and resid 415 through 417 removed outlier: 7.785A pdb=" N LEU D 477 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG D 434 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU D 403 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N TYR D 476 " --> pdb=" O LEU D 403 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL D 405 " --> pdb=" O TYR D 476 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 485 through 487 Processing sheet with id=AD4, first strand: chain 'D' and resid 527 through 529 removed outlier: 4.226A pdb=" N VAL D 527 " --> pdb=" O TYR D 759 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 680 through 681 removed outlier: 6.454A pdb=" N GLY D 681 " --> pdb=" O ILE D 727 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASP D 729 " --> pdb=" O GLY D 681 " (cutoff:3.500A) 1058 hydrogen bonds defined for protein. 3003 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: 9.33 Time building geometry restraints manager: 10.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3897 1.32 - 1.44: 6754 1.44 - 1.57: 13800 1.57 - 1.70: 4 1.70 - 1.83: 217 Bond restraints: 24672 Sorted by residual: bond pdb=" CA SER D 795 " pdb=" C SER D 795 " ideal model delta sigma weight residual 1.520 1.573 -0.053 1.16e-02 7.43e+03 2.11e+01 bond pdb=" C SER D 795 " pdb=" O SER D 795 " ideal model delta sigma weight residual 1.235 1.286 -0.052 1.13e-02 7.83e+03 2.09e+01 bond pdb=" C THR C 665 " pdb=" O THR C 665 " ideal model delta sigma weight residual 1.236 1.291 -0.055 1.28e-02 6.10e+03 1.85e+01 bond pdb=" C1 NAG D 901 " pdb=" O5 NAG D 901 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C THR A 302 " pdb=" O THR A 302 " ideal model delta sigma weight residual 1.234 1.274 -0.040 1.07e-02 8.73e+03 1.39e+01 ... (remaining 24667 not shown) Histogram of bond angle deviations from ideal: 95.26 - 103.12: 194 103.12 - 110.99: 9566 110.99 - 118.85: 10661 118.85 - 126.72: 12652 126.72 - 134.58: 407 Bond angle restraints: 33480 Sorted by residual: angle pdb=" N ILE C 667 " pdb=" CA ILE C 667 " pdb=" C ILE C 667 " ideal model delta sigma weight residual 113.16 101.44 11.72 1.49e+00 4.50e-01 6.19e+01 angle pdb=" C VAL D 431 " pdb=" N PRO D 432 " pdb=" CA PRO D 432 " ideal model delta sigma weight residual 119.85 113.77 6.08 1.01e+00 9.80e-01 3.62e+01 angle pdb=" N GLY C 666 " pdb=" CA GLY C 666 " pdb=" C GLY C 666 " ideal model delta sigma weight residual 112.54 119.21 -6.67 1.28e+00 6.10e-01 2.72e+01 angle pdb=" C ASN B 380 " pdb=" CA ASN B 380 " pdb=" CB ASN B 380 " ideal model delta sigma weight residual 117.23 110.29 6.94 1.36e+00 5.41e-01 2.60e+01 angle pdb=" N GLU A 299 " pdb=" CA GLU A 299 " pdb=" C GLU A 299 " ideal model delta sigma weight residual 109.96 118.00 -8.04 1.58e+00 4.01e-01 2.59e+01 ... (remaining 33475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.98: 14153 25.98 - 51.96: 954 51.96 - 77.94: 128 77.94 - 103.92: 53 103.92 - 129.90: 11 Dihedral angle restraints: 15299 sinusoidal: 6682 harmonic: 8617 Sorted by residual: dihedral pdb=" CB CYS B 745 " pdb=" SG CYS B 745 " pdb=" SG CYS B 800 " pdb=" CB CYS B 800 " ideal model delta sinusoidal sigma weight residual -86.00 -169.00 83.00 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CA TYR D 449 " pdb=" C TYR D 449 " pdb=" N THR D 450 " pdb=" CA THR D 450 " ideal model delta harmonic sigma weight residual 180.00 149.46 30.54 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA PHE B 756 " pdb=" C PHE B 756 " pdb=" N ALA B 757 " pdb=" CA ALA B 757 " ideal model delta harmonic sigma weight residual -180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 15296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 3882 0.224 - 0.448: 7 0.448 - 0.672: 1 0.672 - 0.897: 0 0.897 - 1.121: 1 Chirality restraints: 3891 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.66e+01 chirality pdb=" C1 MAN J 3 " pdb=" O4 NAG J 2 " pdb=" C2 MAN J 3 " pdb=" O5 MAN J 3 " both_signs ideal model delta sigma weight residual False 2.40 2.23 0.17 2.00e-02 2.50e+03 6.95e+01 chirality pdb=" C1 NAG C 804 " pdb=" ND2 ASN C 350 " pdb=" C2 NAG C 804 " pdb=" O5 NAG C 804 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.14e+01 ... (remaining 3888 not shown) Planarity restraints: 4243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 806 " -0.351 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C 806 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C 806 " -0.068 2.00e-02 2.50e+03 pdb=" N2 NAG C 806 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG C 806 " -0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 802 " -0.331 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG C 802 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG C 802 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG C 802 " 0.497 2.00e-02 2.50e+03 pdb=" O7 NAG C 802 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.321 2.00e-02 2.50e+03 2.70e-01 9.12e+02 pdb=" C7 NAG G 1 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.025 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.452 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.227 2.00e-02 2.50e+03 ... (remaining 4240 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 388 2.66 - 3.22: 22705 3.22 - 3.78: 36800 3.78 - 4.34: 49424 4.34 - 4.90: 81855 Nonbonded interactions: 191172 Sorted by model distance: nonbonded pdb=" O THR C 665 " pdb=" OG1 THR C 749 " model vdw 2.097 2.440 nonbonded pdb=" OD1 ASN C 440 " pdb=" N ASP C 441 " model vdw 2.148 2.520 nonbonded pdb=" OG1 THR D 212 " pdb=" OE2 GLU D 239 " model vdw 2.175 2.440 nonbonded pdb=" OG SER A 126 " pdb=" OG SER A 145 " model vdw 2.177 2.440 nonbonded pdb=" OH TYR B 286 " pdb=" OD2 ASP B 294 " model vdw 2.184 2.440 ... (remaining 191167 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 25 through 585 or resid 605 through 798 or resid 801 throu \ gh 808)) selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'O' } 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: 1.230 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: 5.510 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 62.150 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 0.004 0.103 24672 Z= 0.269 Angle : 0.702 13.071 33480 Z= 0.380 Chirality : 0.051 1.121 3891 Planarity : 0.014 0.302 4211 Dihedral : 17.744 129.899 9710 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.09 % Favored : 93.50 % Rotamer: Outliers : 1.20 % Allowed : 19.41 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.21 (0.16), residues: 2954 helix: 1.70 (0.15), residues: 1148 sheet: -0.60 (0.25), residues: 440 loop : -1.66 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 609 HIS 0.013 0.001 HIS A 38 PHE 0.019 0.001 PHE A 197 TYR 0.029 0.001 TYR D 384 ARG 0.011 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 236 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.5144 (OUTLIER) cc_final: 0.4396 (ppp) outliers start: 31 outliers final: 5 residues processed: 263 average time/residue: 0.3677 time to fit residues: 148.6376 Evaluate side-chains 146 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain D residue 666 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 6.9990 chunk 223 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 0.3980 chunk 150 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 231 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 267 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS A 404 HIS B 671 GLN ** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 HIS ** C 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24672 Z= 0.305 Angle : 0.700 12.986 33480 Z= 0.339 Chirality : 0.048 0.363 3891 Planarity : 0.005 0.067 4211 Dihedral : 8.779 101.398 4174 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.06 % Favored : 93.67 % Rotamer: Outliers : 3.38 % Allowed : 19.14 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.17 (0.16), residues: 2954 helix: 1.73 (0.15), residues: 1170 sheet: -0.66 (0.26), residues: 410 loop : -1.64 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 55 HIS 0.008 0.001 HIS A 449 PHE 0.023 0.002 PHE A 554 TYR 0.021 0.002 TYR C 703 ARG 0.017 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 143 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.6786 (mp) REVERT: A 555 MET cc_start: 0.5277 (OUTLIER) cc_final: 0.4487 (ppp) REVERT: A 607 MET cc_start: 0.2058 (ptp) cc_final: 0.1707 (ttm) REVERT: B 40 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7675 (tp) REVERT: C 209 MET cc_start: 0.7107 (mmp) cc_final: 0.6705 (mmm) REVERT: C 641 MET cc_start: 0.6939 (ttp) cc_final: 0.6409 (ttm) REVERT: D 190 TYR cc_start: 0.6200 (OUTLIER) cc_final: 0.5796 (m-80) REVERT: D 529 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8870 (p) REVERT: D 634 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6893 (t80) outliers start: 87 outliers final: 39 residues processed: 216 average time/residue: 0.3463 time to fit residues: 122.0436 Evaluate side-chains 172 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 127 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 609 TRP Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 222 optimal weight: 20.0000 chunk 182 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 268 optimal weight: 0.7980 chunk 289 optimal weight: 3.9990 chunk 239 optimal weight: 9.9990 chunk 266 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 621 ASN C 477 HIS C 796 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24672 Z= 0.206 Angle : 0.563 11.173 33480 Z= 0.282 Chirality : 0.044 0.351 3891 Planarity : 0.004 0.059 4211 Dihedral : 8.054 119.455 4166 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.99 % Favored : 93.74 % Rotamer: Outliers : 2.72 % Allowed : 20.07 % Favored : 77.21 % 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: 0.03 (0.16), residues: 2954 helix: 1.97 (0.15), residues: 1175 sheet: -0.58 (0.26), residues: 414 loop : -1.61 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 55 HIS 0.005 0.001 HIS A 449 PHE 0.021 0.001 PHE B 756 TYR 0.014 0.001 TYR B 286 ARG 0.004 0.000 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 130 time to evaluate : 2.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.6760 (mp) REVERT: A 209 MET cc_start: 0.8305 (tpt) cc_final: 0.8003 (tpt) REVERT: A 238 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8530 (tp) REVERT: A 354 MET cc_start: 0.7382 (mpp) cc_final: 0.6989 (mmm) REVERT: A 555 MET cc_start: 0.5105 (OUTLIER) cc_final: 0.4560 (mmm) REVERT: A 576 MET cc_start: 0.4610 (ppp) cc_final: 0.3924 (tmm) REVERT: B 630 MET cc_start: 0.3796 (ttt) cc_final: 0.3538 (ttm) REVERT: C 101 HIS cc_start: 0.6245 (OUTLIER) cc_final: 0.4931 (m90) REVERT: C 641 MET cc_start: 0.6959 (ttp) cc_final: 0.6448 (ttm) REVERT: D 190 TYR cc_start: 0.6385 (OUTLIER) cc_final: 0.5998 (m-80) REVERT: D 529 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8792 (p) REVERT: D 634 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6907 (t80) REVERT: D 651 MET cc_start: 0.7905 (mmm) cc_final: 0.7327 (mmt) outliers start: 70 outliers final: 33 residues processed: 190 average time/residue: 0.3234 time to fit residues: 103.4121 Evaluate side-chains 165 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 609 TRP Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 757 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 1.9990 chunk 201 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 128 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 269 optimal weight: 0.8980 chunk 285 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 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 162 HIS B 106 GLN C 724 ASN D 28 GLN D 653 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24672 Z= 0.208 Angle : 0.557 9.894 33480 Z= 0.277 Chirality : 0.044 0.356 3891 Planarity : 0.004 0.057 4211 Dihedral : 7.425 114.838 4166 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.19 % Favored : 93.53 % Rotamer: Outliers : 2.87 % Allowed : 19.72 % Favored : 77.41 % 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: 0.12 (0.16), residues: 2954 helix: 2.08 (0.15), residues: 1174 sheet: -0.56 (0.26), residues: 417 loop : -1.58 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 55 HIS 0.003 0.001 HIS A 449 PHE 0.015 0.001 PHE A 458 TYR 0.013 0.001 TYR D 449 ARG 0.005 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 131 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.6711 (mp) REVERT: A 354 MET cc_start: 0.7331 (mpp) cc_final: 0.6974 (mmm) REVERT: A 555 MET cc_start: 0.5033 (mmt) cc_final: 0.4589 (mmm) REVERT: A 576 MET cc_start: 0.4603 (ppp) cc_final: 0.3944 (tmm) REVERT: C 74 MET cc_start: 0.8643 (tpp) cc_final: 0.8278 (tpp) REVERT: C 101 HIS cc_start: 0.6233 (OUTLIER) cc_final: 0.4952 (m90) REVERT: D 190 TYR cc_start: 0.6377 (OUTLIER) cc_final: 0.5996 (m-80) REVERT: D 197 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.6377 (p0) REVERT: D 529 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8746 (p) REVERT: D 634 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6916 (t80) REVERT: D 651 MET cc_start: 0.7957 (mmm) cc_final: 0.7519 (mmt) REVERT: D 831 LEU cc_start: 0.5703 (OUTLIER) cc_final: 0.5445 (tt) outliers start: 74 outliers final: 49 residues processed: 197 average time/residue: 0.3137 time to fit residues: 103.5736 Evaluate side-chains 182 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 126 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 609 TRP Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 811 ASP Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 212 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 243 optimal weight: 0.3980 chunk 197 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 255 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 796 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24672 Z= 0.143 Angle : 0.522 11.383 33480 Z= 0.260 Chirality : 0.043 0.351 3891 Planarity : 0.004 0.059 4211 Dihedral : 6.944 114.233 4163 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.82 % Favored : 93.91 % Rotamer: Outliers : 2.41 % Allowed : 20.57 % Favored : 77.02 % 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: 0.26 (0.16), residues: 2954 helix: 2.23 (0.15), residues: 1175 sheet: -0.52 (0.26), residues: 414 loop : -1.54 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 55 HIS 0.003 0.000 HIS A 449 PHE 0.012 0.001 PHE D 678 TYR 0.012 0.001 TYR D 449 ARG 0.005 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 133 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.6690 (mp) REVERT: A 354 MET cc_start: 0.7202 (mpp) cc_final: 0.6917 (mmm) REVERT: A 555 MET cc_start: 0.5260 (mmt) cc_final: 0.4862 (mmm) REVERT: A 576 MET cc_start: 0.4584 (ppp) cc_final: 0.3961 (tmm) REVERT: B 649 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7889 (tt) REVERT: C 74 MET cc_start: 0.8676 (tpp) cc_final: 0.8272 (tpp) REVERT: C 101 HIS cc_start: 0.6150 (OUTLIER) cc_final: 0.4984 (m90) REVERT: D 190 TYR cc_start: 0.6321 (OUTLIER) cc_final: 0.5986 (m-80) REVERT: D 529 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8690 (p) REVERT: D 634 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6992 (t80) REVERT: D 651 MET cc_start: 0.7889 (mmm) cc_final: 0.7407 (mmt) REVERT: D 831 LEU cc_start: 0.5621 (OUTLIER) cc_final: 0.5365 (tt) outliers start: 62 outliers final: 34 residues processed: 189 average time/residue: 0.3311 time to fit residues: 106.7009 Evaluate side-chains 169 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 128 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 609 TRP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 811 ASP Chi-restraints excluded: chain D residue 831 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 10.0000 chunk 256 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 236 optimal weight: 0.9980 chunk 132 optimal weight: 0.0270 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS C 770 GLN C 796 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24672 Z= 0.275 Angle : 0.578 10.583 33480 Z= 0.290 Chirality : 0.045 0.365 3891 Planarity : 0.004 0.051 4211 Dihedral : 6.882 113.049 4163 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.60 % Favored : 93.13 % Rotamer: Outliers : 2.91 % Allowed : 19.91 % Favored : 77.17 % 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 (0.16), residues: 2954 helix: 2.16 (0.15), residues: 1173 sheet: -0.61 (0.26), residues: 424 loop : -1.51 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP B 55 HIS 0.007 0.001 HIS A 94 PHE 0.019 0.002 PHE C 753 TYR 0.014 0.001 TYR C 410 ARG 0.003 0.000 ARG D 401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 126 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.6731 (mp) REVERT: A 209 MET cc_start: 0.8149 (tpt) cc_final: 0.7593 (tpt) REVERT: A 392 TYR cc_start: 0.6977 (t80) cc_final: 0.6758 (t80) REVERT: A 555 MET cc_start: 0.5306 (mmt) cc_final: 0.4916 (mmm) REVERT: A 576 MET cc_start: 0.4590 (ppp) cc_final: 0.3937 (tmm) REVERT: C 74 MET cc_start: 0.8713 (tpp) cc_final: 0.8203 (tpp) REVERT: C 101 HIS cc_start: 0.6267 (OUTLIER) cc_final: 0.5022 (m90) REVERT: D 190 TYR cc_start: 0.6307 (OUTLIER) cc_final: 0.5837 (m-80) REVERT: D 197 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6520 (p0) REVERT: D 529 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8737 (p) REVERT: D 634 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.7010 (t80) REVERT: D 651 MET cc_start: 0.7984 (mmm) cc_final: 0.7585 (mmt) outliers start: 75 outliers final: 55 residues processed: 192 average time/residue: 0.3079 time to fit residues: 100.2817 Evaluate side-chains 186 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 125 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 811 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 240 optimal weight: 9.9990 chunk 159 optimal weight: 0.7980 chunk 284 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS D 71 ASN 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 : 0.004 0.032 24672 Z= 0.247 Angle : 0.560 12.560 33480 Z= 0.280 Chirality : 0.045 0.363 3891 Planarity : 0.004 0.060 4211 Dihedral : 6.811 112.466 4163 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.60 % Favored : 93.13 % Rotamer: Outliers : 2.95 % Allowed : 20.38 % Favored : 76.67 % 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: 0.15 (0.16), residues: 2954 helix: 2.13 (0.15), residues: 1173 sheet: -0.72 (0.25), residues: 431 loop : -1.53 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.001 TRP B 55 HIS 0.005 0.001 HIS A 94 PHE 0.016 0.001 PHE C 753 TYR 0.011 0.001 TYR D 449 ARG 0.003 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 126 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.6694 (mp) REVERT: A 209 MET cc_start: 0.8161 (tpt) cc_final: 0.7705 (tpt) REVERT: A 354 MET cc_start: 0.7377 (mpp) cc_final: 0.7056 (mmm) REVERT: A 392 TYR cc_start: 0.6879 (t80) cc_final: 0.6675 (t80) REVERT: A 555 MET cc_start: 0.5245 (mmt) cc_final: 0.4840 (mmm) REVERT: A 576 MET cc_start: 0.4642 (ppp) cc_final: 0.4003 (tmm) REVERT: A 709 HIS cc_start: 0.8019 (OUTLIER) cc_final: 0.6715 (p-80) REVERT: A 769 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8262 (ttpp) REVERT: B 630 MET cc_start: 0.3878 (ttt) cc_final: 0.3418 (ppp) REVERT: C 74 MET cc_start: 0.8698 (tpp) cc_final: 0.8173 (tpp) REVERT: C 101 HIS cc_start: 0.6235 (OUTLIER) cc_final: 0.5362 (m90) REVERT: D 190 TYR cc_start: 0.6274 (OUTLIER) cc_final: 0.5815 (m-80) REVERT: D 445 ASP cc_start: 0.1306 (OUTLIER) cc_final: 0.0787 (m-30) REVERT: D 529 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8716 (p) REVERT: D 634 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.7016 (t80) REVERT: D 651 MET cc_start: 0.8026 (mmm) cc_final: 0.7627 (mmt) outliers start: 76 outliers final: 56 residues processed: 193 average time/residue: 0.2833 time to fit residues: 93.1274 Evaluate side-chains 187 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 123 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 811 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 180 optimal weight: 0.6980 chunk 193 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 258 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 492 ASN D 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24672 Z= 0.230 Angle : 0.559 12.679 33480 Z= 0.279 Chirality : 0.044 0.367 3891 Planarity : 0.004 0.056 4211 Dihedral : 6.738 112.777 4163 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.70 % Favored : 93.03 % Rotamer: Outliers : 2.99 % Allowed : 20.77 % Favored : 76.24 % 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: 0.17 (0.16), residues: 2954 helix: 2.18 (0.15), residues: 1173 sheet: -0.74 (0.25), residues: 430 loop : -1.54 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP B 55 HIS 0.013 0.001 HIS A 53 PHE 0.016 0.001 PHE C 753 TYR 0.011 0.001 TYR D 449 ARG 0.002 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 122 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.6733 (mp) REVERT: A 209 MET cc_start: 0.8167 (tpt) cc_final: 0.7710 (tpt) REVERT: A 576 MET cc_start: 0.4524 (ppp) cc_final: 0.3855 (tmm) REVERT: A 641 MET cc_start: 0.7611 (tmm) cc_final: 0.7314 (tmm) REVERT: A 709 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.6774 (p-80) REVERT: A 769 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8249 (ttpp) REVERT: B 630 MET cc_start: 0.3894 (ttt) cc_final: 0.3429 (ppp) REVERT: C 74 MET cc_start: 0.8646 (tpp) cc_final: 0.8129 (tpp) REVERT: C 101 HIS cc_start: 0.6217 (OUTLIER) cc_final: 0.5388 (m90) REVERT: D 190 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.5830 (m-80) REVERT: D 197 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6431 (p0) REVERT: D 445 ASP cc_start: 0.1379 (OUTLIER) cc_final: 0.0917 (m-30) REVERT: D 529 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8726 (p) REVERT: D 634 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6969 (t80) REVERT: D 651 MET cc_start: 0.8113 (mmm) cc_final: 0.7683 (mmt) outliers start: 77 outliers final: 58 residues processed: 192 average time/residue: 0.3081 time to fit residues: 100.1995 Evaluate side-chains 188 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 121 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 811 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 20.0000 chunk 248 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 250 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 280 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 796 GLN D 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24672 Z= 0.235 Angle : 0.567 13.740 33480 Z= 0.283 Chirality : 0.044 0.369 3891 Planarity : 0.004 0.058 4211 Dihedral : 6.695 112.704 4163 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.84 % Favored : 92.89 % Rotamer: Outliers : 2.91 % Allowed : 20.85 % Favored : 76.24 % 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: 0.15 (0.16), residues: 2954 helix: 2.16 (0.15), residues: 1173 sheet: -0.75 (0.25), residues: 430 loop : -1.55 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP B 55 HIS 0.008 0.001 HIS A 53 PHE 0.016 0.001 PHE C 753 TYR 0.012 0.001 TYR D 449 ARG 0.002 0.000 ARG D 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 120 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.6731 (mp) REVERT: A 209 MET cc_start: 0.8173 (tpt) cc_final: 0.7824 (tpt) REVERT: A 392 TYR cc_start: 0.6824 (t80) cc_final: 0.6437 (t80) REVERT: A 576 MET cc_start: 0.4518 (ppp) cc_final: 0.3840 (tmm) REVERT: A 641 MET cc_start: 0.7640 (tmm) cc_final: 0.7338 (tmm) REVERT: A 709 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.6835 (p-80) REVERT: A 769 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8246 (ttpp) REVERT: B 630 MET cc_start: 0.3815 (ttt) cc_final: 0.3396 (ppp) REVERT: C 74 MET cc_start: 0.8641 (tpp) cc_final: 0.8127 (tpp) REVERT: C 101 HIS cc_start: 0.6360 (OUTLIER) cc_final: 0.5591 (m90) REVERT: D 190 TYR cc_start: 0.6259 (OUTLIER) cc_final: 0.5841 (m-80) REVERT: D 197 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6432 (p0) REVERT: D 445 ASP cc_start: 0.1409 (OUTLIER) cc_final: 0.0948 (m-30) REVERT: D 634 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6974 (t80) REVERT: D 651 MET cc_start: 0.8114 (mmm) cc_final: 0.7689 (mmt) outliers start: 75 outliers final: 58 residues processed: 188 average time/residue: 0.3079 time to fit residues: 98.6139 Evaluate side-chains 184 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 118 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 811 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 0.4980 chunk 132 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 293 optimal weight: 0.0070 chunk 270 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 249 optimal weight: 7.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 ASN D 803 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24672 Z= 0.170 Angle : 0.556 13.145 33480 Z= 0.275 Chirality : 0.044 0.366 3891 Planarity : 0.004 0.056 4211 Dihedral : 6.536 112.791 4163 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.57 % Favored : 93.20 % Rotamer: Outliers : 2.48 % Allowed : 21.20 % Favored : 76.32 % 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: 0.21 (0.16), residues: 2954 helix: 2.20 (0.15), residues: 1180 sheet: -0.71 (0.25), residues: 435 loop : -1.52 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP B 55 HIS 0.008 0.001 HIS A 53 PHE 0.013 0.001 PHE A 102 TYR 0.011 0.001 TYR D 449 ARG 0.002 0.000 ARG D 670 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 120 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.6739 (mp) REVERT: A 209 MET cc_start: 0.8102 (tpt) cc_final: 0.7757 (tpt) REVERT: A 576 MET cc_start: 0.4513 (ppp) cc_final: 0.3837 (tmm) REVERT: A 641 MET cc_start: 0.7687 (tmm) cc_final: 0.7400 (tmm) REVERT: A 709 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.6896 (p-80) REVERT: B 384 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8390 (p) REVERT: B 630 MET cc_start: 0.3829 (ttt) cc_final: 0.3400 (ppp) REVERT: C 74 MET cc_start: 0.8638 (tpp) cc_final: 0.8140 (tpp) REVERT: C 101 HIS cc_start: 0.6173 (OUTLIER) cc_final: 0.5347 (m90) REVERT: D 190 TYR cc_start: 0.6290 (OUTLIER) cc_final: 0.5891 (m-80) REVERT: D 197 ASP cc_start: 0.6798 (OUTLIER) cc_final: 0.6398 (p0) REVERT: D 445 ASP cc_start: 0.1396 (OUTLIER) cc_final: 0.0947 (m-30) REVERT: D 634 PHE cc_start: 0.7379 (OUTLIER) cc_final: 0.6967 (t80) REVERT: D 651 MET cc_start: 0.8101 (mmm) cc_final: 0.7658 (mmt) outliers start: 64 outliers final: 49 residues processed: 179 average time/residue: 0.3051 time to fit residues: 92.5173 Evaluate side-chains 175 residues out of total 2576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 118 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 811 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 0.5980 chunk 215 optimal weight: 6.9990 chunk 34 optimal weight: 0.0980 chunk 65 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 205 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.084837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061903 restraints weight = 84539.715| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.59 r_work: 0.3135 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24672 Z= 0.165 Angle : 0.544 12.778 33480 Z= 0.269 Chirality : 0.043 0.365 3891 Planarity : 0.004 0.057 4211 Dihedral : 6.313 112.081 4163 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.87 % Favored : 92.89 % Rotamer: Outliers : 2.45 % Allowed : 21.23 % Favored : 76.32 % 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: 0.27 (0.16), residues: 2954 helix: 2.26 (0.15), residues: 1179 sheet: -0.65 (0.26), residues: 429 loop : -1.50 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP B 55 HIS 0.008 0.001 HIS A 53 PHE 0.013 0.001 PHE D 754 TYR 0.012 0.001 TYR D 449 ARG 0.002 0.000 ARG B 431 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4200.26 seconds wall clock time: 77 minutes 20.83 seconds (4640.83 seconds total)