Starting phenix.real_space_refine on Sat Feb 17 13:47:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2024/8e94_27955_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2024/8e94_27955.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2024/8e94_27955_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2024/8e94_27955_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2024/8e94_27955_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2024/8e94_27955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2024/8e94_27955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2024/8e94_27955_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e94_27955/02_2024/8e94_27955_updated.pdb" } resolution = 3.72 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= 0.010 sd= 0.740 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 80 5.16 5 C 12034 2.51 5 N 3235 2.21 5 O 3467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A ARG 695": "NH1" <-> "NH2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C GLU 528": "OE1" <-> "OE2" Residue "C GLU 712": "OE1" <-> "OE2" Residue "D GLU 239": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18816 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 4710 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 29, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 498 Unresolved non-hydrogen angles: 608 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 11, 'ASP:plan': 15, 'PHE:plan': 1, 'GLU:plan': 35, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 340 Chain: "B" Number of atoms: 4587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 4587 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 38, 'TRANS': 603} Chain breaks: 2 Unresolved non-hydrogen bonds: 402 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 334 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 11, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 5, 'PHE:plan': 4, 'GLU:plan': 17, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 292 Chain: "C" Number of atoms: 4620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 655, 4620 Classifications: {'peptide': 655} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 29, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 595 Unresolved non-hydrogen angles: 726 Unresolved non-hydrogen dihedrals: 496 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 16, 'TYR:plan': 3, 'ASN:plan1': 15, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 31, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 394 Chain: "D" Number of atoms: 4512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4512 Classifications: {'peptide': 638} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 39, 'TRANS': 598} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 547 Unresolved non-hydrogen dihedrals: 367 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 310 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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "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: {'BMA': 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'IWB': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.42, per 1000 atoms: 0.55 Number of scatterers: 18816 At special positions: 0 Unit cell: (131.824, 147.232, 134.392, 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 80 16.00 O 3467 8.00 N 3235 7.00 C 12034 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=1.90 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 317 " distance=2.03 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 453 " distance=2.05 Simple disulfide: pdb=" SG CYS B 433 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.05 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.04 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=1.88 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 798 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM18684 O5 NAG A 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM18469 O5 NAG F 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " BMA F 3 " - " NAG F 4 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A 902 " - " ASN A 276 " " NAG A 903 " - " ASN A 771 " " NAG C 901 " - " ASN C 350 " " NAG C 902 " - " ASN C 203 " " NAG C 903 " - " ASN C 368 " " NAG D 901 " - " ASN D 337 " " NAG E 1 " - " ASN A 61 " " NAG F 1 " - " ASN A 368 " " NAG G 1 " - " ASN B 685 " " NAG H 1 " - " ASN B 337 " " NAG I 1 " - " ASN C 276 " " NAG J 1 " - " ASN C 61 " " NAG K 1 " - " ASN C 771 " Time building additional restraints: 7.60 Conformation dependent library (CDL) restraints added in 3.8 seconds 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4798 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 28 sheets defined 31.8% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 38 through 52 removed outlier: 3.541A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 84 Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.636A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.796A pdb=" N GLN A 147 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 158 " --> pdb=" O MET A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 186 Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 225 through 237 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 279 through 297 removed outlier: 3.968A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 500 through 507 removed outlier: 3.828A pdb=" N LEU A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 526 removed outlier: 4.077A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 673 No H-bonds generated for 'chain 'A' and resid 670 through 673' Processing helix chain 'A' and resid 688 through 694 Processing helix chain 'A' and resid 697 through 708 removed outlier: 5.840A pdb=" N THR A 701 " --> pdb=" O GLU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 722 Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.546A pdb=" N GLU A 739 " --> pdb=" O VAL A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 782 Processing helix chain 'A' and resid 784 through 793 Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 74 through 88 Processing helix chain 'B' and resid 105 through 115 Processing helix chain 'B' and resid 146 through 159 Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.921A pdb=" N ARG B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 217 Processing helix chain 'B' and resid 230 through 242 removed outlier: 4.134A pdb=" N GLU B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N VAL B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 306 removed outlier: 4.043A pdb=" N GLN B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 335 removed outlier: 3.778A pdb=" N TYR B 332 " --> pdb=" O GLU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 666 through 669 No H-bonds generated for 'chain 'B' and resid 666 through 669' Processing helix chain 'B' and resid 688 through 695 Processing helix chain 'B' and resid 697 through 702 Processing helix chain 'B' and resid 711 through 720 removed outlier: 3.621A pdb=" N THR B 716 " --> pdb=" O GLU B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 738 Processing helix chain 'B' and resid 769 through 783 removed outlier: 3.533A pdb=" N ASP B 774 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 775 " --> pdb=" O ARG B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 793 removed outlier: 3.806A pdb=" N LEU B 789 " --> pdb=" O GLU B 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 52 Processing helix chain 'C' and resid 71 through 83 Processing helix chain 'C' and resid 105 through 112 Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 144 through 157 Processing helix chain 'C' and resid 171 through 187 removed outlier: 4.214A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 225 through 237 removed outlier: 4.231A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 258 through 261 No H-bonds generated for 'chain 'C' and resid 258 through 261' Processing helix chain 'C' and resid 279 through 298 removed outlier: 4.383A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'C' and resid 458 through 470 removed outlier: 3.701A pdb=" N THR C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 521 through 524 No H-bonds generated for 'chain 'C' and resid 521 through 524' Processing helix chain 'C' and resid 670 through 673 No H-bonds generated for 'chain 'C' and resid 670 through 673' Processing helix chain 'C' and resid 688 through 695 Processing helix chain 'C' and resid 698 through 708 removed outlier: 4.513A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 722 Processing helix chain 'C' and resid 733 through 742 Processing helix chain 'C' and resid 768 through 782 removed outlier: 3.846A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 792 Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 74 through 88 Processing helix chain 'D' and resid 105 through 115 Processing helix chain 'D' and resid 146 through 160 removed outlier: 3.926A pdb=" N VAL D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 153 " --> pdb=" O GLN D 149 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 187 removed outlier: 3.744A pdb=" N ARG D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 217 Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'D' and resid 285 through 304 Processing helix chain 'D' and resid 326 through 335 Processing helix chain 'D' and resid 457 through 469 Processing helix chain 'D' and resid 493 through 499 Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 666 through 669 No H-bonds generated for 'chain 'D' and resid 666 through 669' Processing helix chain 'D' and resid 687 through 695 removed outlier: 4.207A pdb=" N ASN D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 704 removed outlier: 4.087A pdb=" N VAL D 704 " --> pdb=" O HIS D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 720 Processing helix chain 'D' and resid 730 through 736 removed outlier: 3.701A pdb=" N TYR D 735 " --> pdb=" O ALA D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 783 removed outlier: 3.934A pdb=" N ALA D 772 " --> pdb=" O HIS D 768 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 775 " --> pdb=" O ARG D 771 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA D 776 " --> pdb=" O ALA D 772 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP D 783 " --> pdb=" O GLN D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 793 Processing sheet with id= A, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= B, first strand: chain 'A' and resid 193 through 197 Processing sheet with id= C, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.793A pdb=" N GLY A 268 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 397 through 402 removed outlier: 6.427A pdb=" N THR A 473 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE A 400 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU A 475 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N THR A 402 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N HIS A 477 " --> pdb=" O THR A 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 409 through 412 Processing sheet with id= F, first strand: chain 'A' and resid 534 through 537 removed outlier: 4.089A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 728 through 732 removed outlier: 4.471A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.180A pdb=" N VAL B 32 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL B 67 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL B 34 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 197 through 200 removed outlier: 6.749A pdb=" N VAL B 251 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ALA B 226 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 253 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.885A pdb=" N GLY B 373 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA B 362 " --> pdb=" O MET B 371 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N MET B 371 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 405 through 407 removed outlier: 3.511A pdb=" N TYR B 476 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR B 407 " --> pdb=" O TYR B 476 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 414 through 417 removed outlier: 3.508A pdb=" N GLU B 417 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 453 " --> pdb=" O GLU B 417 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 531 through 535 Processing sheet with id= N, first strand: chain 'C' and resid 26 through 33 removed outlier: 6.382A pdb=" N GLN C 59 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE C 29 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN C 61 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N ALA C 31 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C 63 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N LEU C 33 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL C 65 " --> pdb=" O LEU C 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 90 through 92 Processing sheet with id= P, first strand: chain 'C' and resid 194 through 197 removed outlier: 6.718A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C 222 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL C 246 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N LEU C 221 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU C 248 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 268 through 271 removed outlier: 4.227A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN C 357 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU C 361 " --> pdb=" O GLN C 357 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 397 through 402 removed outlier: 6.150A pdb=" N THR C 473 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ILE C 400 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU C 475 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N THR C 402 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N HIS C 477 " --> pdb=" O THR C 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 409 through 412 Processing sheet with id= T, first strand: chain 'C' and resid 486 through 489 Processing sheet with id= U, first strand: chain 'C' and resid 534 through 536 removed outlier: 4.488A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 536 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 729 through 732 removed outlier: 3.990A pdb=" N PHE C 729 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 32 through 34 removed outlier: 7.137A pdb=" N GLY D 92 " --> pdb=" O ALA D 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'D' and resid 197 through 201 removed outlier: 3.714A pdb=" N LEU D 201 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 274 through 277 removed outlier: 3.659A pdb=" N GLY D 373 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA D 362 " --> pdb=" O MET D 371 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N MET D 371 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 402 through 407 removed outlier: 6.782A pdb=" N SER D 472 " --> pdb=" O LEU D 403 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL D 405 " --> pdb=" O SER D 472 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP D 474 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N THR D 407 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR D 476 " --> pdb=" O THR D 407 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'D' and resid 414 through 417 Processing sheet with id= AB, first strand: chain 'D' and resid 531 through 534 581 hydrogen bonds defined for protein. 1596 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: 6.03 Time building geometry restraints manager: 8.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2971 1.29 - 1.43: 5205 1.43 - 1.58: 10949 1.58 - 1.72: 0 1.72 - 1.86: 124 Bond restraints: 19249 Sorted by residual: bond pdb=" C7 IWB B 901 " pdb=" N6 IWB B 901 " ideal model delta sigma weight residual 1.585 1.331 0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C11 IWB B 901 " pdb=" C12 IWB B 901 " ideal model delta sigma weight residual 1.528 1.357 0.171 2.00e-02 2.50e+03 7.29e+01 bond pdb=" C24 IWB B 901 " pdb=" N6 IWB B 901 " ideal model delta sigma weight residual 1.498 1.349 0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" C PRO D 388 " pdb=" O PRO D 388 " ideal model delta sigma weight residual 1.233 1.150 0.083 1.23e-02 6.61e+03 4.53e+01 bond pdb=" C PRO D 396 " pdb=" O PRO D 396 " ideal model delta sigma weight residual 1.234 1.166 0.067 1.08e-02 8.57e+03 3.88e+01 ... (remaining 19244 not shown) Histogram of bond angle deviations from ideal: 96.24 - 104.02: 359 104.02 - 111.80: 9654 111.80 - 119.58: 6580 119.58 - 127.36: 9539 127.36 - 135.14: 251 Bond angle restraints: 26383 Sorted by residual: angle pdb=" C GLY D 260 " pdb=" N SER D 261 " pdb=" CA SER D 261 " ideal model delta sigma weight residual 120.28 130.71 -10.43 1.34e+00 5.57e-01 6.06e+01 angle pdb=" CA ARG B 411 " pdb=" C ARG B 411 " pdb=" N PRO B 412 " ideal model delta sigma weight residual 120.77 128.29 -7.52 9.70e-01 1.06e+00 6.01e+01 angle pdb=" C PRO D 396 " pdb=" CA PRO D 396 " pdb=" CB PRO D 396 " ideal model delta sigma weight residual 110.85 100.12 10.73 1.41e+00 5.03e-01 5.79e+01 angle pdb=" C ILE A 133 " pdb=" CA ILE A 133 " pdb=" CB ILE A 133 " ideal model delta sigma weight residual 111.80 120.57 -8.77 1.18e+00 7.18e-01 5.52e+01 angle pdb=" CA VAL A 246 " pdb=" C VAL A 246 " pdb=" O VAL A 246 " ideal model delta sigma weight residual 120.22 113.74 6.48 8.90e-01 1.26e+00 5.30e+01 ... (remaining 26378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.35: 10739 23.35 - 46.71: 741 46.71 - 70.06: 93 70.06 - 93.41: 28 93.41 - 116.76: 14 Dihedral angle restraints: 11615 sinusoidal: 4164 harmonic: 7451 Sorted by residual: dihedral pdb=" C ARG B 411 " pdb=" N ARG B 411 " pdb=" CA ARG B 411 " pdb=" CB ARG B 411 " ideal model delta harmonic sigma weight residual -122.60 -150.21 27.61 0 2.50e+00 1.60e-01 1.22e+02 dihedral pdb=" N ARG B 411 " pdb=" C ARG B 411 " pdb=" CA ARG B 411 " pdb=" CB ARG B 411 " ideal model delta harmonic sigma weight residual 122.80 149.13 -26.33 0 2.50e+00 1.60e-01 1.11e+02 dihedral pdb=" CB CYS C 420 " pdb=" SG CYS C 420 " pdb=" SG CYS C 454 " pdb=" CB CYS C 454 " ideal model delta sinusoidal sigma weight residual 93.00 28.63 64.37 1 1.00e+01 1.00e-02 5.45e+01 ... (remaining 11612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.817: 3213 0.817 - 1.635: 3 1.635 - 2.452: 0 2.452 - 3.269: 1 3.269 - 4.086: 1 Chirality restraints: 3218 Sorted by residual: chirality pdb=" C1 NAG F 4 " pdb=" O4 BMA F 3 " pdb=" C2 NAG F 4 " pdb=" O5 NAG F 4 " both_signs ideal model delta sigma weight residual False -2.40 -1.29 -1.11 2.00e-02 2.50e+03 3.09e+03 chirality pdb=" C7 IWB B 901 " pdb=" C18 IWB B 901 " pdb=" C8 IWB B 901 " pdb=" N6 IWB B 901 " both_signs ideal model delta sigma weight residual False -2.70 1.38 -4.09 2.00e-01 2.50e+01 4.17e+02 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-02 2.50e+03 3.14e+02 ... (remaining 3215 not shown) Planarity restraints: 3354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 4 " 0.354 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG F 4 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG F 4 " 0.108 2.00e-02 2.50e+03 pdb=" N2 NAG F 4 " -0.541 2.00e-02 2.50e+03 pdb=" O7 NAG F 4 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.318 2.00e-02 2.50e+03 2.76e-01 9.54e+02 pdb=" C7 NAG J 1 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.485 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 901 " 0.322 2.00e-02 2.50e+03 2.74e-01 9.36e+02 pdb=" C7 NAG A 901 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A 901 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG A 901 " -0.478 2.00e-02 2.50e+03 pdb=" O7 NAG A 901 " 0.054 2.00e-02 2.50e+03 ... (remaining 3351 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 19 2.23 - 2.89: 7762 2.89 - 3.56: 24962 3.56 - 4.23: 37042 4.23 - 4.90: 64272 Nonbonded interactions: 134057 Sorted by model distance: nonbonded pdb=" NE1 TRP D 304 " pdb=" O GLY D 308 " model vdw 1.557 2.520 nonbonded pdb=" ND2 ASN A 350 " pdb=" O5 NAG A 901 " model vdw 1.761 2.520 nonbonded pdb=" OD1 ASP B 97 " pdb=" N ASN B 98 " model vdw 1.845 2.520 nonbonded pdb=" NE1 TRP D 304 " pdb=" C GLY D 308 " model vdw 1.968 3.350 nonbonded pdb=" CD1 ILE A 220 " pdb=" CD1 LEU A 248 " model vdw 1.992 3.880 ... (remaining 134052 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 26 and (name N or name CA or name C or name O \ or name CB )) or resid 27 through 34 or (resid 35 through 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 or (resid 42 through 45 and (n \ ame N or name CA or name C or name O or name CB )) or resid 46 or (resid 47 thro \ ugh 52 and (name N or name CA or name C or name O or name CB )) or resid 53 thro \ ugh 55 or (resid 56 through 57 and (name N or name CA or name C or name O or nam \ e CB )) or resid 58 through 82 or (resid 83 and (name N or name CA or name C or \ name O or name CB )) or resid 84 through 98 or (resid 99 through 100 and (name N \ or name CA or name C or name O or name CB )) or resid 101 through 129 or (resid \ 130 through 131 and (name N or name CA or name C or name O or name CB )) or res \ id 132 through 158 or (resid 159 and (name N or name CA or name C or name O or n \ ame CB )) or resid 160 through 192 or (resid 193 and (name N or name CA or name \ C or name O or name CB )) or resid 194 through 211 or (resid 212 through 213 and \ (name N or name CA or name C or name O or name CB )) or resid 214 through 236 o \ r (resid 237 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 38 through 239 or (resid 240 and (name N or name CA or name C or name O or name \ CB )) or resid 241 through 250 or (resid 251 through 253 and (name N or name CA \ or name C or name O or name CB )) or resid 254 through 272 or (resid 273 and (na \ me N or name CA or name C or name O or name CB )) or resid 274 through 292 or (r \ esid 293 through 294 and (name N or name CA or name C or name O or name CB )) or \ resid 295 through 305 or (resid 306 and (name N or name CA or name C or name O \ or name CB )) or resid 307 through 322 or (resid 323 and (name N or name CA or n \ ame C or name O or name CB )) or resid 324 through 325 or (resid 326 and (name N \ or name CA or name C or name O or name CB )) or resid 327 through 342 or (resid \ 343 and (name N or name CA or name C or name O or name CB )) or (resid 344 thro \ ugh 347 and (name N or name CA or name C or name O or name CB )) or resid 348 th \ rough 359 or (resid 360 and (name N or name CA or name C or name O or name CB )) \ or resid 361 through 370 or (resid 371 and (name N or name CA or name C or name \ O or name CB )) or resid 372 through 376 or (resid 377 through 379 and (name N \ or name CA or name C or name O or name CB )) or resid 380 through 387 or (resid \ 388 and (name N or name CA or name C or name O or name CB )) or resid 389 or (re \ sid 390 and (name N or name CA or name C or name O or name CB )) or resid 391 th \ rough 414 or (resid 415 and (name N or name CA or name C or name O or name CB )) \ or resid 416 through 418 or (resid 419 and (name N or name CA or name C or name \ O or name CB )) or resid 420 through 421 or (resid 422 through 423 and (name N \ or name CA or name C or name O or name CB )) or resid 424 through 441 or (resid \ 442 through 443 and (name N or name CA or name C or name O or name CB )) or resi \ d 444 through 445 or (resid 446 and (name N or name CA or name C or name O or na \ me CB )) or resid 447 through 666 or (resid 667 through 669 and (name N or name \ CA or name C or name O or name CB )) or resid 670 through 672 or (resid 673 thro \ ugh 674 and (name N or name CA or name C or name O or name CB )) or resid 675 th \ rough 678 or (resid 679 and (name N or name CA or name C or name O or name CB )) \ or resid 680 or (resid 681 through 682 and (name N or name CA or name C or name \ O or name CB )) or resid 683 through 684 or (resid 685 and (name N or name CA o \ r name C or name O or name CB )) or resid 686 through 693 or (resid 694 and (nam \ e N or name CA or name C or name O or name CB )) or resid 695 through 702 or (re \ sid 703 through 704 and (name N or name CA or name C or name O or name CB )) or \ resid 705 through 718 or (resid 719 through 721 and (name N or name CA or name C \ or name O or name CB )) or resid 722 through 723 or (resid 724 through 728 and \ (name N or name CA or name C or name O or name CB )) or resid 729 through 751 or \ (resid 752 and (name N or name CA or name C or name O or name CB )) or resid 75 \ 3 through 788 or (resid 789 through 790 and (name N or name CA or name C or name \ O or name CB )) or resid 791 through 797 or resid 901 through 903)) selection = (chain 'C' and (resid 25 through 47 or (resid 48 through 52 and (name N or name \ CA or name C or name O or name CB )) or resid 53 through 155 or (resid 156 and ( \ name N or name CA or name C or name O or name CB )) or resid 157 through 177 or \ (resid 178 and (name N or name CA or name C or name O or name CB )) or resid 179 \ through 189 or (resid 190 through 193 and (name N or name CA or name C or name \ O or name CB )) or resid 194 through 214 or (resid 215 through 216 and (name N o \ r name CA or name C or name O or name CB )) or resid 217 through 224 or (resid 2 \ 25 and (name N or name CA or name C or name O or name CB )) or resid 226 through \ 259 or (resid 260 and (name N or name CA or name C or name O or name CB )) or r \ esid 261 through 271 or (resid 272 through 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 289 or (resid 290 through 291 and ( \ name N or name CA or name C or name O or name CB )) or resid 292 through 296 or \ (resid 297 through 303 and (name N or name CA or name C or name O or name CB )) \ or resid 304 through 336 or (resid 337 and (name N or name CA or name C or name \ O or name CB )) or resid 338 or (resid 339 and (name N or name CA or name C or n \ ame O or name CB )) or resid 340 or (resid 341 through 343 and (name N or name C \ A or name C or name O or name CB )) or (resid 344 through 347 and (name N or nam \ e CA or name C or name O or name CB )) or resid 348 through 366 or (resid 367 an \ d (name N or name CA or name C or name O or name CB )) or resid 368 through 378 \ or (resid 379 and (name N or name CA or name C or name O or name CB )) or resid \ 380 through 425 or (resid 426 through 427 and (name N or name CA or name C or na \ me O or name CB )) or resid 428 through 503 or (resid 504 and (name N or name CA \ or name C or name O or name CB )) or resid 505 through 519 or (resid 520 and (n \ ame N or name CA or name C or name O or name CB )) or resid 521 through 540 or ( \ resid 541 and (name N or name CA or name C or name O or name CB )) or resid 542 \ through 663 or (resid 664 through 665 and (name N or name CA or name C or name O \ or name CB )) or (resid 666 through 669 and (name N or name CA or name C or nam \ e O or name CB )) or resid 670 through 696 or (resid 697 through 699 and (name N \ or name CA or name C or name O or name CB )) or resid 700 through 701 or (resid \ 702 through 704 and (name N or name CA or name C or name O or name CB )) or res \ id 705 through 741 or (resid 742 through 743 and (name N or name CA or name C or \ name O or name CB )) or resid 744 through 786 or (resid 787 and (name N or name \ CA or name C or name O or name CB )) or resid 788 through 797 or resid 901 thro \ ugh 903)) } ncs_group { reference = (chain 'B' and (resid 31 through 53 or (resid 54 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 72 or (resid 73 and (na \ me N or name CA or name C or name O or name CB )) or resid 74 through 88 or (res \ id 89 and (name N or name CA or name C or name O or name CB )) or resid 90 throu \ gh 96 or (resid 97 through 103 and (name N or name CA or name C or name O or nam \ e CB )) or resid 104 through 132 or (resid 133 through 134 and (name N or name C \ A or name C or name O or name CB )) or resid 135 through 157 or (resid 158 and ( \ name N or name CA or name C or name O or name CB )) or resid 159 through 160 or \ (resid 161 and (name N or name CA or name C or name O or name CB )) or resid 162 \ through 179 or (resid 180 and (name N or name CA or name C or name O or name CB \ )) or resid 181 through 182 or (resid 183 through 184 and (name N or name CA or \ name C or name O or name CB )) or resid 185 through 186 or (resid 187 through 1 \ 88 and (name N or name CA or name C or name O or name CB )) or resid 189 or (res \ id 190 and (name N or name CA or name C or name O or name CB )) or resid 191 thr \ ough 202 or (resid 203 and (name N or name CA or name C or name O or name CB )) \ or resid 204 through 216 or (resid 217 and (name N or name CA or name C or name \ O or name CB )) or resid 218 through 219 or (resid 220 through 221 and (name N o \ r name CA or name C or name O or name CB )) or resid 222 through 231 or (resid 2 \ 32 through 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 241 or (resid 242 through 243 and (name N or name CA or name C or n \ ame O or name CB )) or resid 244 through 256 or (resid 257 through 258 and (name \ N or name CA or name C or name O or name CB )) or resid 259 through 281 or (res \ id 282 and (name N or name CA or name C or name O or name CB )) or resid 283 thr \ ough 284 or (resid 285 through 287 and (name N or name CA or name C or name O or \ name CB )) or resid 288 through 305 or (resid 306 through 307 and (name N or na \ me CA or name C or name O or name CB )) or resid 308 through 327 or (resid 328 t \ hrough 330 and (name N or name CA or name C or name O or name CB )) or resid 331 \ through 343 or (resid 344 and (name N or name CA or name C or name O or name CB \ )) or resid 345 through 363 or (resid 364 through 365 and (name N or name CA or \ name C or name O or name CB )) or resid 366 through 408 or (resid 409 through 4 \ 10 and (name N or name CA or name C or name O or name CB )) or resid 411 through \ 416 or (resid 417 and (name N or name CA or name C or name O or name CB )) or r \ esid 418 through 435 or (resid 436 and (name N or name CA or name C or name O or \ name CB )) or resid 437 or (resid 447 through 449 and (name N or name CA or nam \ e C or name O or name CB )) or resid 450 or (resid 451 and (name N or name CA or \ name C or name O or name CB )) or resid 452 through 481 or (resid 482 and (name \ N or name CA or name C or name O or name CB )) or resid 483 through 496 or (res \ id 497 and (name N or name CA or name C or name O or name CB )) or resid 498 thr \ ough 500 or (resid 501 and (name N or name CA or name C or name O or name CB )) \ or resid 502 through 537 or resid 659 through 667 or (resid 668 through 670 and \ (name N or name CA or name C or name O or name CB )) or resid 671 through 696 or \ (resid 697 and (name N or name CA or name C or name O or name CB )) or resid 69 \ 8 or (resid 699 through 700 and (name N or name CA or name C or name O or name C \ B )) or resid 701 or (resid 702 through 703 and (name N or name CA or name C or \ name O or name CB )) or resid 704 through 705 or (resid 706 through 709 and (nam \ e N or name CA or name C or name O or name CB )) or resid 710 through 723 or (re \ sid 724 through 725 and (name N or name CA or name C or name O or name CB )) or \ resid 726 through 773 or (resid 774 and (name N or name CA or name C or name O o \ r name CB )) or resid 775 through 798)) selection = (chain 'D' and (resid 31 through 54 or (resid 55 through 58 and (name N or name \ CA or name C or name O or name CB )) or resid 59 through 262 or (resid 263 throu \ gh 264 and (name N or name CA or name C or name O or name CB )) or resid 265 thr \ ough 278 or (resid 279 and (name N or name CA or name C or name O or name CB )) \ or resid 280 through 285 or (resid 286 through 287 and (name N or name CA or nam \ e C or name O or name CB )) or resid 288 through 297 or (resid 298 and (name N o \ r name CA or name C or name O or name CB )) or resid 299 through 304 or (resid 3 \ 05 through 307 and (name N or name CA or name C or name O or name CB )) or resid \ 308 through 364 or (resid 365 and (name N or name CA or name C or name O or nam \ e CB )) or resid 366 through 373 or (resid 374 and (name N or name CA or name C \ or name O or name CB )) or resid 375 or (resid 376 and (name N or name CA or nam \ e C or name O or name CB )) or resid 377 through 389 or (resid 390 and (name N o \ r name CA or name C or name O or name CB )) or resid 391 or (resid 399 and (name \ N or name CA or name C or name O or name CB )) or resid 400 through 433 or (res \ id 434 and (name N or name CA or name C or name O or name CB )) or resid 435 thr \ ough 448 or (resid 449 and (name N or name CA or name C or name O or name CB )) \ or resid 450 through 454 or (resid 455 and (name N or name CA or name C or name \ O or name CB )) or resid 456 through 514 or (resid 515 and (name N or name CA or \ name C or name O or name CB )) or resid 516 through 527 or (resid 528 and (name \ N or name CA or name C or name O or name CB )) or resid 529 through 664 or (res \ id 665 through 670 and (name N or name CA or name C or name O or name CB )) or r \ esid 671 through 672 or (resid 673 through 675 and (name N or name CA or name C \ or name O or name CB )) or resid 676 through 679 or (resid 680 and (name N or na \ me CA or name C or name O or name CB )) or resid 681 through 712 or (resid 713 t \ hrough 714 and (name N or name CA or name C or name O or name CB )) or resid 715 \ through 796 or (resid 797 and (name N or name CA or name C or name O or name CB \ )) or resid 798)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'J' } 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 group one per residue 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.380 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 51.920 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.160 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.254 19249 Z= 0.383 Angle : 0.927 17.684 26383 Z= 0.535 Chirality : 0.110 4.086 3218 Planarity : 0.016 0.304 3341 Dihedral : 16.387 116.764 6781 Min Nonbonded Distance : 1.557 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.48 % Favored : 91.32 % Rotamer: Outliers : 1.27 % Allowed : 20.66 % Favored : 78.08 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.16), residues: 2570 helix: -0.07 (0.18), residues: 829 sheet: -2.09 (0.24), residues: 411 loop : -2.76 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 387 HIS 0.011 0.001 HIS A 705 PHE 0.032 0.001 PHE C 458 TYR 0.058 0.001 TYR D 390 ARG 0.004 0.000 ARG B 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 185 average time/residue: 0.2711 time to fit residues: 80.7005 Evaluate side-chains 172 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 161 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 392 TYR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 768 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 201 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 HIS A 239 ASN A 705 HIS A 709 HIS D 80 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19249 Z= 0.241 Angle : 0.694 11.065 26383 Z= 0.340 Chirality : 0.048 0.450 3218 Planarity : 0.005 0.070 3341 Dihedral : 10.651 106.306 3315 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.91 % Favored : 91.05 % Rotamer: Outliers : 4.83 % Allowed : 20.66 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.16), residues: 2570 helix: 0.19 (0.18), residues: 844 sheet: -1.99 (0.25), residues: 383 loop : -2.71 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 731 HIS 0.006 0.001 HIS D 175 PHE 0.027 0.002 PHE C 458 TYR 0.033 0.001 TYR A 703 ARG 0.006 0.000 ARG B 411 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 171 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8697 (p) REVERT: A 277 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7764 (tm-30) REVERT: A 542 VAL cc_start: 0.7171 (p) cc_final: 0.6904 (m) REVERT: C 356 LEU cc_start: 0.6926 (tp) cc_final: 0.6454 (tt) outliers start: 84 outliers final: 49 residues processed: 235 average time/residue: 0.2773 time to fit residues: 107.1070 Evaluate side-chains 209 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 159 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 724 ASP Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 429 ASN Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 766 ASP Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 129 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 chunk 208 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 187 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19249 Z= 0.327 Angle : 0.707 10.166 26383 Z= 0.353 Chirality : 0.049 0.581 3218 Planarity : 0.005 0.090 3341 Dihedral : 9.885 96.575 3311 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.86 % Favored : 89.11 % Rotamer: Outliers : 6.79 % Allowed : 22.15 % Favored : 71.06 % 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: -2.38 (0.16), residues: 2570 helix: 0.15 (0.18), residues: 848 sheet: -2.00 (0.25), residues: 389 loop : -2.71 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 304 HIS 0.006 0.001 HIS A 94 PHE 0.027 0.002 PHE C 458 TYR 0.023 0.002 TYR A 392 ARG 0.004 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 166 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8677 (p) REVERT: A 261 TYR cc_start: 0.6694 (OUTLIER) cc_final: 0.4394 (p90) REVERT: A 277 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 502 MET cc_start: 0.8329 (tpp) cc_final: 0.8070 (tpp) REVERT: A 542 VAL cc_start: 0.7326 (p) cc_final: 0.7044 (m) REVERT: B 467 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7633 (ttp80) REVERT: B 685 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8564 (p0) REVERT: C 695 ARG cc_start: 0.5890 (OUTLIER) cc_final: 0.5422 (ttp80) REVERT: C 712 GLU cc_start: 0.7397 (tp30) cc_final: 0.7179 (tp30) outliers start: 118 outliers final: 78 residues processed: 261 average time/residue: 0.2605 time to fit residues: 110.9147 Evaluate side-chains 237 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 154 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 467 ARG Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 685 ASN Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 724 ASP Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 695 ARG Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 429 ASN Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 766 ASP Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 773 ILE Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 231 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 121 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 234 optimal weight: 0.5980 chunk 248 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 222 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19249 Z= 0.157 Angle : 0.605 10.578 26383 Z= 0.298 Chirality : 0.045 0.423 3218 Planarity : 0.004 0.072 3341 Dihedral : 8.775 86.013 3309 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.63 % Favored : 92.33 % Rotamer: Outliers : 4.03 % Allowed : 25.20 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.16), residues: 2570 helix: 0.58 (0.18), residues: 849 sheet: -1.70 (0.26), residues: 370 loop : -2.49 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 304 HIS 0.005 0.001 HIS C 705 PHE 0.017 0.001 PHE C 458 TYR 0.018 0.001 TYR A 392 ARG 0.004 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 183 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8615 (tpp) cc_final: 0.8350 (tpp) REVERT: A 277 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7564 (tm-30) REVERT: A 502 MET cc_start: 0.8192 (tpp) cc_final: 0.7957 (tpp) REVERT: A 542 VAL cc_start: 0.7106 (p) cc_final: 0.6759 (m) REVERT: B 467 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7590 (ttp80) REVERT: C 356 LEU cc_start: 0.6922 (tp) cc_final: 0.6543 (tt) REVERT: D 269 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7878 (m-10) outliers start: 70 outliers final: 45 residues processed: 239 average time/residue: 0.2567 time to fit residues: 100.2796 Evaluate side-chains 212 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 165 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 467 ARG Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 766 ASP Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 206 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 171 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19249 Z= 0.312 Angle : 0.671 10.778 26383 Z= 0.336 Chirality : 0.047 0.378 3218 Planarity : 0.005 0.072 3341 Dihedral : 8.773 77.799 3304 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 7.13 % Allowed : 23.48 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.16), residues: 2570 helix: 0.44 (0.18), residues: 844 sheet: -1.82 (0.26), residues: 389 loop : -2.51 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 375 HIS 0.005 0.001 HIS D 175 PHE 0.021 0.002 PHE C 458 TYR 0.023 0.002 TYR A 392 ARG 0.004 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 163 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.4983 (p90) REVERT: A 502 MET cc_start: 0.8257 (tpp) cc_final: 0.7944 (tpp) REVERT: A 506 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8196 (mm) REVERT: B 685 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8614 (p0) REVERT: C 356 LEU cc_start: 0.7026 (tp) cc_final: 0.6536 (tt) REVERT: D 269 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7912 (m-10) REVERT: D 382 MET cc_start: 0.8445 (mmt) cc_final: 0.8197 (mmm) outliers start: 124 outliers final: 96 residues processed: 262 average time/residue: 0.2446 time to fit residues: 105.2978 Evaluate side-chains 258 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 158 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 685 ASN Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 429 ASN Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 766 ASP Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 773 ILE Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 145 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 206 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19249 Z= 0.166 Angle : 0.601 12.507 26383 Z= 0.297 Chirality : 0.045 0.330 3218 Planarity : 0.004 0.071 3341 Dihedral : 8.266 69.508 3304 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.70 % Favored : 92.26 % Rotamer: Outliers : 5.18 % Allowed : 25.49 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.17), residues: 2570 helix: 0.63 (0.19), residues: 846 sheet: -1.68 (0.27), residues: 360 loop : -2.37 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 56 HIS 0.006 0.001 HIS C 477 PHE 0.016 0.001 PHE C 458 TYR 0.019 0.001 TYR A 392 ARG 0.002 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 171 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.4168 (p90) REVERT: A 277 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7561 (tm-30) REVERT: A 502 MET cc_start: 0.8151 (tpp) cc_final: 0.7877 (tpp) REVERT: B 203 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7935 (pp) REVERT: B 467 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7593 (ttp80) REVERT: B 685 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8629 (p0) REVERT: C 154 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8377 (ptm) REVERT: C 356 LEU cc_start: 0.7027 (tp) cc_final: 0.6564 (tt) REVERT: D 269 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7812 (m-10) REVERT: D 786 THR cc_start: 0.9109 (m) cc_final: 0.8887 (m) outliers start: 90 outliers final: 70 residues processed: 243 average time/residue: 0.2739 time to fit residues: 109.4915 Evaluate side-chains 237 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 161 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 467 ARG Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 685 ASN Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 729 ASP Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 766 ASP Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 239 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 141 optimal weight: 7.9990 chunk 181 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 209 optimal weight: 0.0010 chunk 138 optimal weight: 3.9990 chunk 247 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19249 Z= 0.145 Angle : 0.583 12.226 26383 Z= 0.288 Chirality : 0.045 0.366 3218 Planarity : 0.004 0.070 3341 Dihedral : 7.909 67.586 3303 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 5.01 % Allowed : 26.35 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.17), residues: 2570 helix: 0.80 (0.19), residues: 849 sheet: -1.58 (0.27), residues: 362 loop : -2.28 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 56 HIS 0.023 0.001 HIS C 477 PHE 0.014 0.001 PHE C 458 TYR 0.018 0.001 TYR A 703 ARG 0.002 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 173 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 TYR cc_start: 0.6380 (OUTLIER) cc_final: 0.3802 (p90) REVERT: A 366 ILE cc_start: 0.8507 (mm) cc_final: 0.8122 (mt) REVERT: A 442 THR cc_start: 0.6117 (OUTLIER) cc_final: 0.5851 (p) REVERT: A 502 MET cc_start: 0.8107 (tpp) cc_final: 0.7831 (tpp) REVERT: B 203 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7893 (pp) REVERT: B 467 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7625 (ttp80) REVERT: B 685 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8622 (p0) REVERT: B 723 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7927 (mp) REVERT: C 154 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8344 (ptm) REVERT: C 356 LEU cc_start: 0.7021 (tp) cc_final: 0.6574 (tt) REVERT: C 451 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.7823 (m) REVERT: D 269 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7765 (m-10) REVERT: D 786 THR cc_start: 0.9083 (m) cc_final: 0.8844 (m) outliers start: 87 outliers final: 63 residues processed: 241 average time/residue: 0.2616 time to fit residues: 101.8455 Evaluate side-chains 234 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 162 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 467 ARG Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 685 ASN Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 704 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 766 ASP Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 157 optimal weight: 0.5980 chunk 168 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN D 141 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19249 Z= 0.322 Angle : 0.668 11.762 26383 Z= 0.334 Chirality : 0.047 0.421 3218 Planarity : 0.005 0.074 3341 Dihedral : 8.227 63.271 3301 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 6.10 % Allowed : 25.32 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.17), residues: 2570 helix: 0.57 (0.18), residues: 849 sheet: -1.79 (0.26), residues: 391 loop : -2.34 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 56 HIS 0.006 0.001 HIS D 175 PHE 0.021 0.002 PHE D 154 TYR 0.023 0.002 TYR A 392 ARG 0.006 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 156 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8624 (tpp) cc_final: 0.8375 (tpp) REVERT: A 261 TYR cc_start: 0.6635 (OUTLIER) cc_final: 0.5107 (p90) REVERT: A 442 THR cc_start: 0.6263 (OUTLIER) cc_final: 0.5961 (p) REVERT: B 203 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8061 (pp) REVERT: B 685 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8558 (p0) REVERT: B 723 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8126 (mp) REVERT: C 154 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8339 (ptm) REVERT: D 269 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7815 (m-10) outliers start: 106 outliers final: 84 residues processed: 242 average time/residue: 0.2582 time to fit residues: 102.1144 Evaluate side-chains 244 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 153 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 536 GLN Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 685 ASN Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 429 ASN Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 659 THR Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 766 ASP Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 225 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 230 optimal weight: 0.4980 chunk 138 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 181 optimal weight: 0.0570 chunk 70 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 218 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19249 Z= 0.158 Angle : 0.593 11.764 26383 Z= 0.293 Chirality : 0.045 0.397 3218 Planarity : 0.004 0.072 3341 Dihedral : 7.733 65.976 3301 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.78 % Favored : 92.18 % Rotamer: Outliers : 4.83 % Allowed : 26.35 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.17), residues: 2570 helix: 0.74 (0.18), residues: 857 sheet: -1.56 (0.27), residues: 371 loop : -2.23 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 56 HIS 0.005 0.001 HIS C 705 PHE 0.014 0.001 PHE C 458 TYR 0.017 0.001 TYR A 392 ARG 0.003 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 168 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8599 (tpp) cc_final: 0.8391 (tpp) REVERT: A 261 TYR cc_start: 0.6396 (OUTLIER) cc_final: 0.4128 (p90) REVERT: A 442 THR cc_start: 0.6290 (OUTLIER) cc_final: 0.6010 (p) REVERT: A 502 MET cc_start: 0.8114 (tpp) cc_final: 0.7847 (tpp) REVERT: B 203 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7967 (pp) REVERT: B 454 CYS cc_start: 0.6584 (m) cc_final: 0.6314 (m) REVERT: B 467 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7632 (ttp80) REVERT: B 685 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8588 (p0) REVERT: B 723 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7999 (mp) REVERT: C 154 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8334 (ptm) REVERT: C 356 LEU cc_start: 0.7014 (tp) cc_final: 0.6561 (tt) REVERT: C 451 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7840 (m) REVERT: D 269 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7765 (m-10) REVERT: D 786 THR cc_start: 0.9101 (m) cc_final: 0.8874 (m) outliers start: 84 outliers final: 71 residues processed: 235 average time/residue: 0.2695 time to fit residues: 102.7080 Evaluate side-chains 240 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 160 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 247 TRP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 467 ARG Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 685 ASN Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 766 ASP Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 244 optimal weight: 0.0470 chunk 148 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 157 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 overall best weight: 1.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19249 Z= 0.172 Angle : 0.585 12.779 26383 Z= 0.289 Chirality : 0.045 0.417 3218 Planarity : 0.004 0.098 3341 Dihedral : 7.488 65.309 3301 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 5.24 % Allowed : 25.83 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.17), residues: 2570 helix: 0.83 (0.18), residues: 856 sheet: -1.50 (0.26), residues: 398 loop : -2.19 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 56 HIS 0.004 0.001 HIS C 705 PHE 0.026 0.001 PHE B 95 TYR 0.019 0.001 TYR A 392 ARG 0.004 0.000 ARG A 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 164 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8595 (tpp) cc_final: 0.8376 (tpp) REVERT: A 261 TYR cc_start: 0.6433 (OUTLIER) cc_final: 0.4301 (p90) REVERT: A 442 THR cc_start: 0.6285 (OUTLIER) cc_final: 0.5975 (p) REVERT: A 502 MET cc_start: 0.8113 (tpp) cc_final: 0.7911 (tpp) REVERT: B 203 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7897 (pp) REVERT: B 454 CYS cc_start: 0.6691 (m) cc_final: 0.6422 (m) REVERT: B 467 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7642 (ttp80) REVERT: B 685 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8599 (p0) REVERT: B 723 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7993 (mp) REVERT: C 154 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8333 (ptm) REVERT: C 356 LEU cc_start: 0.6972 (tp) cc_final: 0.6520 (tt) REVERT: C 451 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.7899 (m) REVERT: D 269 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7806 (m-10) REVERT: D 786 THR cc_start: 0.9082 (m) cc_final: 0.8843 (m) outliers start: 91 outliers final: 76 residues processed: 236 average time/residue: 0.2598 time to fit residues: 100.9575 Evaluate side-chains 244 residues out of total 2218 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 159 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 440 THR Chi-restraints excluded: chain B residue 467 ARG Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 685 ASN Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 766 ASP Chi-restraints excluded: chain B residue 798 CYS Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 748 ILE Chi-restraints excluded: chain D residue 766 ASP Chi-restraints excluded: chain D residue 768 HIS Chi-restraints excluded: chain D residue 791 THR Chi-restraints excluded: chain D residue 797 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 187 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 25 optimal weight: 0.0010 chunk 37 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108243 restraints weight = 42232.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110016 restraints weight = 27935.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111210 restraints weight = 21300.880| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19249 Z= 0.160 Angle : 0.575 12.309 26383 Z= 0.284 Chirality : 0.045 0.414 3218 Planarity : 0.004 0.097 3341 Dihedral : 7.321 65.220 3301 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 5.12 % Allowed : 26.29 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2570 helix: 0.89 (0.18), residues: 855 sheet: -1.40 (0.26), residues: 402 loop : -2.14 (0.17), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 56 HIS 0.004 0.001 HIS C 705 PHE 0.016 0.001 PHE D 154 TYR 0.018 0.001 TYR A 392 ARG 0.004 0.000 ARG A 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3539.41 seconds wall clock time: 65 minutes 37.77 seconds (3937.77 seconds total)