Starting phenix.real_space_refine on Fri Feb 6 11:15:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pzs_72078/02_2026/9pzs_72078.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pzs_72078/02_2026/9pzs_72078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pzs_72078/02_2026/9pzs_72078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pzs_72078/02_2026/9pzs_72078.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pzs_72078/02_2026/9pzs_72078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pzs_72078/02_2026/9pzs_72078.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 15441 2.51 5 N 4082 2.21 5 O 4668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24307 Number of models: 1 Model: "" Number of chains: 19 Chain: "D" Number of atoms: 4873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 4873 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'PTRANS': 23, 'TRANS': 656} Chain breaks: 6 Unresolved non-hydrogen bonds: 520 Unresolved non-hydrogen angles: 639 Unresolved non-hydrogen dihedrals: 438 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ASP:plan': 15, 'GLU:plan': 24, 'HIS:plan': 4, 'PHE:plan': 5, 'ARG:plan': 10, 'ASN:plan1': 6, 'GLN:plan1': 8, 'TYR:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 328 Chain: "A" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5081 Classifications: {'peptide': 691} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 29, 'TRANS': 661} Chain breaks: 4 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 506 Unresolved non-hydrogen dihedrals: 362 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 17, 'GLN:plan1': 5, 'GLU:plan': 11, 'TRP:plan': 3, 'HIS:plan': 3, 'ASP:plan': 7, 'PHE:plan': 4, 'ASN:plan1': 5, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 258 Chain: "F" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 744 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 2, 'PHE:plan': 4, 'TYR:plan': 6, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 116 Chain: "G" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 755 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 108} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 4, 'GLN:plan1': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 4892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 4892 Classifications: {'peptide': 672} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 22, 'TRANS': 649} Chain breaks: 5 Unresolved non-hydrogen bonds: 447 Unresolved non-hydrogen angles: 563 Unresolved non-hydrogen dihedrals: 387 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'HIS:plan': 3, 'ASP:plan': 9, 'GLU:plan': 16, 'ARG:plan': 10, 'ASN:plan1': 6, 'PHE:plan': 7, 'GLN:plan1': 5, 'TYR:plan': 5, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 298 Chain: "C" Number of atoms: 4925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 4925 Classifications: {'peptide': 693} Incomplete info: {'truncation_to_alanine': 140} Link IDs: {'PTRANS': 29, 'TRANS': 663} Chain breaks: 3 Unresolved non-hydrogen bonds: 583 Unresolved non-hydrogen angles: 708 Unresolved non-hydrogen dihedrals: 501 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'ARG:plan': 20, 'ASP:plan': 8, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 21, 'TYR:plan': 6, 'ASN:plan1': 9, 'GLN:plan1': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 356 Chain: "J" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 689 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain breaks: 2 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 6, 'TYR:plan': 4, 'GLU:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "K" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 628 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 93} Chain breaks: 2 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 744 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 2, 'TRANS': 116} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 2, 'PHE:plan': 4, 'TYR:plan': 6, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 116 Chain: "I" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 755 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 108} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 4, 'GLN:plan1': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 80 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "P" 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: 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 Chain: "B" 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 Chain: "C" 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: 5.73, per 1000 atoms: 0.24 Number of scatterers: 24307 At special positions: 0 Unit cell: (181.22, 203.524, 177.038, 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 116 16.00 O 4668 8.00 N 4082 7.00 C 15441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS F 42 " - pdb=" SG CYS F 116 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 115 " distance=2.04 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 112 " distance=2.03 Simple disulfide: pdb=" SG CYS H 42 " - pdb=" SG CYS H 116 " distance=2.03 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 114 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A1001 " - " ASN A 300 " " NAG B1501 " - " ASN B 340 " " NAG C1001 " - " ASN C 276 " " NAG E 1 " - " ASN D 341 " " NAG L 1 " - " ASN D 688 " " NAG M 1 " - " ASN A 61 " " NAG N 1 " - " ASN A 276 " " NAG O 1 " - " ASN B 687 " " NAG P 1 " - " ASN C 61 " Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.2 seconds 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6334 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 45 sheets defined 33.8% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'D' and resid 46 through 53 Processing helix chain 'D' and resid 77 through 93 removed outlier: 3.525A pdb=" N ILE D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 119 removed outlier: 4.152A pdb=" N PHE D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.833A pdb=" N PHE D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 259 through 264 removed outlier: 4.125A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 325 through 329 removed outlier: 3.685A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 329' Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.520A pdb=" N ILE D 464 " --> pdb=" O PHE D 460 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL D 472 " --> pdb=" O ILE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 517 through 522 removed outlier: 3.717A pdb=" N GLU D 521 " --> pdb=" O GLU D 518 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL D 522 " --> pdb=" O ARG D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 614 removed outlier: 3.920A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 656 removed outlier: 3.706A pdb=" N MET D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE D 655 " --> pdb=" O ALA D 651 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN D 656 " --> pdb=" O ALA D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 697 Processing helix chain 'D' and resid 699 through 706 Processing helix chain 'D' and resid 707 through 710 removed outlier: 4.103A pdb=" N ASN D 710 " --> pdb=" O GLY D 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 707 through 710' Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 772 through 787 removed outlier: 3.578A pdb=" N LEU D 778 " --> pdb=" O ARG D 774 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 779 " --> pdb=" O GLN D 775 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE D 780 " --> pdb=" O VAL D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 4.321A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 50 removed outlier: 4.086A pdb=" N ASN A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.778A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 186 removed outlier: 3.987A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.522A pdb=" N ASP A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.514A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 256 through 261 removed outlier: 4.006A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 261' Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.613A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.655A pdb=" N ALA A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 615 removed outlier: 3.818A pdb=" N LEU A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 657 removed outlier: 3.781A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 668 removed outlier: 4.068A pdb=" N ASN A 668 " --> pdb=" O THR A 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.529A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.660A pdb=" N GLU A 707 " --> pdb=" O TYR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 769 through 782 removed outlier: 3.792A pdb=" N ASN A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'G' and resid 105 through 109 Processing helix chain 'G' and resid 118 through 122 removed outlier: 3.658A pdb=" N LEU G 122 " --> pdb=" O GLY G 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.634A pdb=" N SER B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.719A pdb=" N GLN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.802A pdb=" N ALA B 131 " --> pdb=" O HIS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 179 through 192 removed outlier: 3.638A pdb=" N PHE B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 removed outlier: 3.584A pdb=" N GLN B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 247 removed outlier: 3.683A pdb=" N VAL B 237 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 310 removed outlier: 3.973A pdb=" N GLU B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS B 309 " --> pdb=" O SER B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 472 removed outlier: 3.662A pdb=" N ILE B 463 " --> pdb=" O PHE B 459 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 501 Processing helix chain 'B' and resid 515 through 522 removed outlier: 3.995A pdb=" N VAL B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 522 " --> pdb=" O ARG B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 614 removed outlier: 4.106A pdb=" N PHE B 613 " --> pdb=" O TRP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 655 removed outlier: 3.786A pdb=" N GLN B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.513A pdb=" N TYR B 676 " --> pdb=" O PRO B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 698 removed outlier: 4.091A pdb=" N ARG B 692 " --> pdb=" O GLY B 688 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN B 693 " --> pdb=" O SER B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 707 removed outlier: 4.205A pdb=" N LYS B 707 " --> pdb=" O GLN B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 723 Processing helix chain 'B' and resid 732 through 741 removed outlier: 3.515A pdb=" N ARG B 741 " --> pdb=" O TYR B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 784 removed outlier: 4.651A pdb=" N GLN B 774 " --> pdb=" O PRO B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 796 removed outlier: 3.507A pdb=" N LEU B 791 " --> pdb=" O GLU B 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 removed outlier: 4.104A pdb=" N ASN C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.596A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 159 removed outlier: 3.529A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 188 removed outlier: 3.800A pdb=" N ARG C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.828A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 removed outlier: 3.730A pdb=" N ARG C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 297 Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 628 through 657 removed outlier: 3.527A pdb=" N LEU C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.660A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 769 through 782 removed outlier: 3.648A pdb=" N ASN C 782 " --> pdb=" O LYS C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'I' and resid 105 through 109 Processing helix chain 'I' and resid 118 through 122 removed outlier: 3.658A pdb=" N LEU I 122 " --> pdb=" O GLY I 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 67 through 73 removed outlier: 6.318A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE D 126 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N LEU D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 198 through 205 removed outlier: 7.314A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU D 205 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR D 173 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE D 168 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LEU D 229 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER D 170 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N TYR D 231 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 228 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE D 257 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 230 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 475 through 480 removed outlier: 3.898A pdb=" N ASP D 477 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET D 508 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP D 524 " --> pdb=" O ILE D 766 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 418 through 421 removed outlier: 3.869A pdb=" N GLY D 451 " --> pdb=" O ILE D 440 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.549A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.549A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR D 532 " --> pdb=" O SER D 759 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N SER D 759 " --> pdb=" O THR D 532 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 757 " --> pdb=" O ILE D 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 59 through 65 removed outlier: 6.132A pdb=" N VAL A 27 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR A 63 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL A 65 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N TYR A 88 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N ASN A 28 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE A 90 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLY A 30 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A 92 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL A 32 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 164 through 167 removed outlier: 6.942A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.376A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 478 removed outlier: 3.987A pdb=" N MET A 512 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 401 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.525A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 488 through 490 removed outlier: 3.986A pdb=" N LYS A 495 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 517 through 518 removed outlier: 3.878A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 681 through 682 Processing sheet with id=AB6, first strand: chain 'A' and resid 681 through 682 removed outlier: 4.474A pdb=" N LEU A 538 " --> pdb=" O PHE A 754 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE A 754 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 23 through 26 removed outlier: 3.510A pdb=" N THR F 98 " --> pdb=" O ASP F 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 30 through 31 removed outlier: 6.385A pdb=" N GLU F 30 " --> pdb=" O THR F 139 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N TYR F 53 " --> pdb=" O GLU F 119 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE F 54 " --> pdb=" O TRP F 70 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP F 70 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP F 56 " --> pdb=" O ILE F 68 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 30 through 31 removed outlier: 6.385A pdb=" N GLU F 30 " --> pdb=" O THR F 139 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N CYS F 116 " --> pdb=" O TYR F 131 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR F 131 " --> pdb=" O CYS F 116 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG F 118 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N PHE F 129 " --> pdb=" O ARG F 118 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY F 120 " --> pdb=" O ALA F 127 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 24 through 27 removed outlier: 3.546A pdb=" N ASP G 96 " --> pdb=" O SER G 93 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 30 through 32 removed outlier: 6.354A pdb=" N LEU G 31 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLN G 63 " --> pdb=" O LEU G 72 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU G 72 " --> pdb=" O GLN G 63 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 50 through 51 removed outlier: 3.727A pdb=" N ASN G 56 " --> pdb=" O TRP G 51 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 68 through 74 removed outlier: 3.590A pdb=" N LEU B 40 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU B 98 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 199 through 205 removed outlier: 9.170A pdb=" N PHE B 170 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N ILE B 204 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU B 172 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 228 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B 279 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL B 363 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 406 through 410 removed outlier: 3.742A pdb=" N ILE B 408 " --> pdb=" O ASP B 476 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AC8, first strand: chain 'B' and resid 523 through 524 Processing sheet with id=AC9, first strand: chain 'B' and resid 530 through 531 Processing sheet with id=AD1, first strand: chain 'B' and resid 533 through 537 removed outlier: 6.525A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ASP B 731 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 59 through 65 removed outlier: 3.712A pdb=" N ASN C 61 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE C 29 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR C 63 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 193 through 195 Processing sheet with id=AD4, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.556A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 473 through 478 removed outlier: 4.156A pdb=" N THR C 402 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N MET C 512 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL C 514 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 409 through 412 removed outlier: 3.744A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 681 through 682 removed outlier: 7.180A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.700A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 681 through 682 removed outlier: 7.180A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.700A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU C 538 " --> pdb=" O PHE C 754 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N PHE C 754 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 23 through 25 removed outlier: 3.532A pdb=" N GLN J 24 " --> pdb=" O LYS J 42 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL J 37 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU J 102 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE J 39 " --> pdb=" O MET J 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET J 100 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR J 97 " --> pdb=" O ASP J 92 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 77 through 79 removed outlier: 4.161A pdb=" N GLY J 68 " --> pdb=" O TRP J 55 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA J 134 " --> pdb=" O TYR J 113 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 24 through 27 removed outlier: 3.511A pdb=" N THR K 25 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER K 27 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER K 42 " --> pdb=" O SER K 27 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER K 89 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN K 98 " --> pdb=" O SER K 87 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER K 87 " --> pdb=" O ASN K 98 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 77 through 78 removed outlier: 6.575A pdb=" N TRP K 59 " --> pdb=" O LEU K 71 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR K 73 " --> pdb=" O MET K 57 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET K 57 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE K 111 " --> pdb=" O TYR K 60 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET K 109 " --> pdb=" O GLN K 62 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 23 through 26 removed outlier: 3.510A pdb=" N THR H 98 " --> pdb=" O ASP H 93 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 30 through 31 removed outlier: 6.385A pdb=" N GLU H 30 " --> pdb=" O THR H 139 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N TYR H 53 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE H 54 " --> pdb=" O TRP H 70 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP H 70 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP H 56 " --> pdb=" O ILE H 68 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 30 through 31 removed outlier: 6.385A pdb=" N GLU H 30 " --> pdb=" O THR H 139 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N CYS H 116 " --> pdb=" O TYR H 131 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR H 131 " --> pdb=" O CYS H 116 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG H 118 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N PHE H 129 " --> pdb=" O ARG H 118 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY H 120 " --> pdb=" O ALA H 127 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 24 through 27 removed outlier: 3.545A pdb=" N ASP I 96 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 30 through 32 removed outlier: 6.354A pdb=" N LEU I 31 " --> pdb=" O GLU I 133 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLN I 63 " --> pdb=" O LEU I 72 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU I 72 " --> pdb=" O GLN I 63 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 50 through 51 removed outlier: 3.726A pdb=" N ASN I 56 " --> pdb=" O TRP I 51 " (cutoff:3.500A) 1055 hydrogen bonds defined for protein. 2964 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.54 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7850 1.34 - 1.46: 4130 1.46 - 1.58: 12637 1.58 - 1.70: 0 1.70 - 1.82: 184 Bond restraints: 24801 Sorted by residual: bond pdb=" N VAL D 522 " pdb=" CA VAL D 522 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.18e-02 7.18e+03 1.32e+01 bond pdb=" N VAL C 490 " pdb=" CA VAL C 490 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.30e-02 5.92e+03 8.46e+00 bond pdb=" N GLU D 272 " pdb=" CA GLU D 272 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.34e+00 bond pdb=" N PHE D 681 " pdb=" CA PHE D 681 " ideal model delta sigma weight residual 1.453 1.488 -0.034 1.22e-02 6.72e+03 7.87e+00 bond pdb=" N ARG D 682 " pdb=" CA ARG D 682 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.51e+00 ... (remaining 24796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 32828 1.43 - 2.87: 936 2.87 - 4.30: 161 4.30 - 5.74: 13 5.74 - 7.17: 2 Bond angle restraints: 33940 Sorted by residual: angle pdb=" N VAL D 522 " pdb=" CA VAL D 522 " pdb=" C VAL D 522 " ideal model delta sigma weight residual 112.96 109.14 3.82 1.00e+00 1.00e+00 1.46e+01 angle pdb=" C THR C 791 " pdb=" N TRP C 792 " pdb=" CA TRP C 792 " ideal model delta sigma weight residual 122.58 115.41 7.17 2.07e+00 2.33e-01 1.20e+01 angle pdb=" N VAL A 204 " pdb=" CA VAL A 204 " pdb=" C VAL A 204 " ideal model delta sigma weight residual 112.17 108.96 3.21 9.50e-01 1.11e+00 1.14e+01 angle pdb=" CA LYS D 473 " pdb=" C LYS D 473 " pdb=" O LYS D 473 " ideal model delta sigma weight residual 122.03 117.81 4.22 1.25e+00 6.40e-01 1.14e+01 angle pdb=" CA VAL C 490 " pdb=" C VAL C 490 " pdb=" O VAL C 490 " ideal model delta sigma weight residual 121.58 118.27 3.31 1.00e+00 1.00e+00 1.09e+01 ... (remaining 33935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 14265 21.29 - 42.57: 355 42.57 - 63.86: 47 63.86 - 85.15: 10 85.15 - 106.43: 6 Dihedral angle restraints: 14683 sinusoidal: 4861 harmonic: 9822 Sorted by residual: dihedral pdb=" CA TYR D 164 " pdb=" C TYR D 164 " pdb=" N ASP D 165 " pdb=" CA ASP D 165 " ideal model delta harmonic sigma weight residual 180.00 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" O4 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C5 BMA M 3 " pdb=" O5 BMA M 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.72 106.43 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C3 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C5 BMA M 3 " pdb=" O5 BMA M 3 " ideal model delta sinusoidal sigma weight residual 47.62 -57.07 104.69 1 3.00e+01 1.11e-03 1.34e+01 ... (remaining 14680 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3618 0.071 - 0.142: 452 0.142 - 0.213: 8 0.213 - 0.284: 2 0.284 - 0.356: 1 Chirality restraints: 4081 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.45e+01 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.32e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.02e+01 ... (remaining 4078 not shown) Planarity restraints: 4358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.343 2.00e-02 2.50e+03 2.97e-01 1.11e+03 pdb=" C7 NAG L 1 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.530 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " -0.323 2.00e-02 2.50e+03 2.75e-01 9.49e+02 pdb=" C7 NAG O 1 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " 0.482 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1001 " 0.310 2.00e-02 2.50e+03 2.65e-01 8.75e+02 pdb=" C7 NAG A1001 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A1001 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG A1001 " -0.461 2.00e-02 2.50e+03 pdb=" O7 NAG A1001 " 0.052 2.00e-02 2.50e+03 ... (remaining 4355 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 174 2.55 - 3.14: 19342 3.14 - 3.73: 37118 3.73 - 4.31: 47694 4.31 - 4.90: 79091 Nonbonded interactions: 183419 Sorted by model distance: nonbonded pdb=" CG2 ILE C 527 " pdb=" O MET C 762 " model vdw 1.965 3.460 nonbonded pdb=" NH2 ARG C 377 " pdb=" O TYR H 123 " model vdw 2.050 3.120 nonbonded pdb=" CG2 ILE A 527 " pdb=" O MET A 762 " model vdw 2.113 3.460 nonbonded pdb=" OH TYR D 479 " pdb=" OE1 GLU D 500 " model vdw 2.144 3.040 nonbonded pdb=" CD1 LEU D 62 " pdb=" CG1 VAL D 64 " model vdw 2.163 3.880 ... (remaining 183414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 152 or (resid 153 through 156 and (name N or na \ me CA or name C or name O or name CB )) or resid 157 or (resid 158 and (name N o \ r name CA or name C or name O or name CB )) or resid 159 through 160 or (resid 1 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 162 through \ 168 or (resid 169 and (name N or name CA or name C or name O or name CB )) or r \ esid 170 through 173 or (resid 174 through 176 and (name N or name CA or name C \ or name O or name CB )) or resid 177 through 178 or (resid 179 and (name N or na \ me CA or name C or name O or name CB )) or resid 180 or (resid 181 and (name N o \ r name CA or name C or name O or name CB )) or resid 182 through 186 or (resid 1 \ 87 through 188 and (name N or name CA or name C or name O or name CB )) or resid \ 189 through 209 or (resid 210 through 211 and (name N or name CA or name C or n \ ame O or name CB )) or resid 212 through 236 or (resid 237 and (name N or name C \ A or name C or name O or name CB )) or resid 238 through 250 or (resid 251 and ( \ name N or name CA or name C or name O or name CB )) or resid 252 through 258 or \ (resid 259 through 260 and (name N or name CA or name C or name O or name CB )) \ or resid 261 through 299 or (resid 300 and (name N or name CA or name C or name \ O or name CB )) or resid 301 through 342 or (resid 343 and (name N or name CA or \ name C or name O or name CB )) or resid 344 through 359 or (resid 360 through 3 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 362 through \ 384 or (resid 385 through 388 and (name N or name CA or name C or name O or nam \ e CB )) or resid 389 or (resid 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 through 393 or (resid 394 and (name N or name CA or nam \ e C or name O or name CB )) or resid 395 through 396 or (resid 397 and (name N o \ r name CA or name C or name O or name CB )) or resid 398 or (resid 399 and (name \ N or name CA or name C or name O or name CB )) or resid 400 through 482 or (res \ id 483 and (name N or name CA or name C or name O or name CB )) or resid 484 thr \ ough 485 or (resid 486 and (name N or name CA or name C or name O or name CB )) \ or resid 487 or (resid 488 through 497 and (name N or name CA or name C or name \ O or name CB )) or resid 498 through 503 or (resid 504 and (name N or name CA or \ name C or name O or name CB )) or resid 505 through 508 or (resid 509 through 5 \ 10 and (name N or name CA or name C or name O or name CB )) or resid 511 through \ 524 or (resid 525 and (name N or name CA or name C or name O or name CB )) or r \ esid 526 through 543 or resid 609 or (resid 610 through 611 and (name N or name \ CA or name C or name O or name CB )) or resid 612 through 627 or (resid 628 thro \ ugh 630 and (name N or name CA or name C or name O or name CB )) or resid 631 th \ rough 633 or (resid 634 through 637 and (name N or name CA or name C or name O o \ r name CB )) or (resid 638 through 655 and (name N or name CA or name C or name \ O or name CB )) or resid 656 through 658 or (resid 664 and (name N or name CA or \ name C or name O or name CB )) or resid 665 through 666 or (resid 667 through 6 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 669 through \ 672 or (resid 673 through 674 and (name N or name CA or name C or name O or nam \ e CB )) or resid 675 or (resid 676 through 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 na \ me CA or name C or name O or name CB )) or resid 683 through 684 or (resid 685 t \ hrough 686 and (name N or name CA or name C or name O or name CB )) or resid 687 \ through 700 or (resid 701 through 709 and (name N or name CA or name C or name \ O or name CB )) or resid 710 or (resid 711 through 712 and (name N or name CA or \ name C or name O or name CB )) or resid 713 through 715 or (resid 716 through 7 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 718 or (res \ id 719 through 720 and (name N or name CA or name C or name O or name CB )) or r \ esid 721 or (resid 722 and (name N or name CA or name C or name O or name CB )) \ or resid 723 through 724 or (resid 725 and (name N or name CA or name C or name \ O or name CB )) or resid 726 through 742 or (resid 743 and (name N or name CA or \ name C or name O or name CB )) or resid 744 through 747 or (resid 748 and (name \ N or name CA or name C or name O or name CB )) or resid 749 through 750 or (res \ id 751 and (name N or name CA or name C or name O or name CB )) or resid 752 thr \ ough 768 or (resid 769 and (name N or name CA or name C or name O or name CB )) \ or resid 770 through 785 or (resid 786 and (name N or name CA or name C or name \ O or name CB )) or resid 787 through 789 or (resid 790 and (name N or name CA or \ name C or name O or name CB )) or resid 791 through 793 or (resid 794 through 7 \ 96 and (name N or name CA or name C or name O or name CB )) or resid 797 through \ 1001)) selection = (chain 'C' and (resid 25 through 35 or (resid 36 through 37 and (name N or name \ CA or name C or name O or name CB )) or resid 38 through 39 or (resid 40 through \ 41 and (name N or name CA or name C or name O or name CB )) or resid 42 or (res \ id 43 through 45 and (name N or name CA or name C or name O or name CB )) or res \ id 46 through 47 or (resid 48 through 49 and (name N or name CA or name C or nam \ e O or name CB )) or resid 50 through 54 or (resid 55 through 57 and (name N or \ name CA or name C or name O or name CB )) or resid 58 through 93 or (resid 94 an \ d (name N or name CA or name C or name O or name CB )) or resid 95 through 201 o \ r (resid 202 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 03 through 269 or (resid 270 and (name N or name CA or name C or name O or name \ CB )) or resid 271 through 272 or (resid 273 and (name N or name CA or name C or \ name O or name CB )) or resid 274 through 293 or (resid 294 and (name N or name \ CA or name C or name O or name CB )) or resid 295 through 296 or (resid 297 thr \ ough 300 and (name N or name CA or name C or name O or name CB )) or resid 301 t \ hrough 305 or (resid 306 and (name N or name CA or name C or name O or name CB ) \ ) or resid 307 through 312 or (resid 313 and (name N or name CA or name C or nam \ e O or name CB )) or resid 314 through 321 or (resid 322 through 323 and (name N \ or name CA or name 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 throu \ gh 331 or (resid 332 and (name N or name CA or name C or name O or name CB )) or \ resid 333 or resid 337 through 338 or (resid 339 and (name N or name CA or name \ C or name O or name CB )) or resid 340 through 356 or (resid 357 and (name N or \ name CA or name C or name O or name CB )) or resid 358 through 362 or (resid 36 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 364 through \ 376 or (resid 377 through 378 and (name N or name CA or name C or name O or name \ CB )) or resid 379 through 426 or (resid 427 and (name N or name CA or name C o \ r name O or name CB )) or resid 428 or (resid 429 and (name N or name CA or name \ C or name O or name CB )) or resid 430 through 447 or (resid 448 and (name N or \ name CA or name C or name O or name CB )) or resid 449 through 613 or (resid 61 \ 4 through 630 and (name N or name CA or name C or name O or name CB )) or resid \ 631 through 635 or (resid 636 through 637 and (name N or name CA or name C or na \ me O or name CB )) or resid 638 through 694 or (resid 695 and (name N or name CA \ or name C or name O or name CB )) or resid 696 or (resid 697 through 698 and (n \ ame N or name CA or name C or name O or name CB )) or resid 699 through 1001)) } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' } 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: 2.970 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: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 24.510 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.269 24833 Z= 0.227 Angle : 0.595 7.169 34020 Z= 0.362 Chirality : 0.043 0.356 4081 Planarity : 0.012 0.297 4349 Dihedral : 10.084 106.432 8301 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.14 % Allowed : 6.13 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 3349 helix: 0.99 (0.17), residues: 1016 sheet: -0.49 (0.20), residues: 699 loop : -1.24 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 124 TYR 0.010 0.001 TYR J 114 PHE 0.011 0.001 PHE A 533 TRP 0.012 0.001 TRP C 315 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00321 (24801) covalent geometry : angle 0.59049 (33940) SS BOND : bond 0.00216 ( 16) SS BOND : angle 0.47882 ( 32) hydrogen bonds : bond 0.23377 ( 1033) hydrogen bonds : angle 7.94196 ( 2964) link_BETA1-4 : bond 0.00204 ( 7) link_BETA1-4 : angle 0.76926 ( 21) link_NAG-ASN : bond 0.11936 ( 9) link_NAG-ASN : angle 2.74682 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 277 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.1596 (ppp) cc_final: 0.0437 (ttt) REVERT: D 464 ILE cc_start: 0.8841 (mt) cc_final: 0.8460 (tp) REVERT: D 503 MET cc_start: 0.7909 (mmm) cc_final: 0.7381 (tpp) REVERT: A 177 GLN cc_start: 0.8941 (tt0) cc_final: 0.8574 (pp30) REVERT: A 218 VAL cc_start: 0.7446 (t) cc_final: 0.7201 (t) REVERT: A 354 MET cc_start: 0.8472 (mmm) cc_final: 0.7916 (mmm) REVERT: A 501 MET cc_start: 0.6376 (mtm) cc_final: 0.6116 (mtm) REVERT: A 742 GLN cc_start: 0.6675 (mm-40) cc_final: 0.6452 (mt0) REVERT: B 112 MET cc_start: 0.6330 (mmm) cc_final: 0.6096 (mmt) REVERT: B 475 TYR cc_start: 0.5394 (p90) cc_final: 0.5036 (p90) REVERT: B 782 PHE cc_start: 0.9008 (m-10) cc_final: 0.8531 (m-80) REVERT: C 501 MET cc_start: 0.5758 (mtm) cc_final: 0.5074 (ptp) REVERT: I 86 ASP cc_start: 0.6503 (p0) cc_final: 0.6300 (p0) outliers start: 3 outliers final: 1 residues processed: 280 average time/residue: 0.1393 time to fit residues: 65.7245 Evaluate side-chains 171 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 20.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN D 159 ASN D 348 ASN D 483 ASN D 672 GLN D 694 ASN ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 449 HIS A 477 HIS ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 GLN ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN B 154 GLN B 335 HIS B 358 HIS C 50 ASN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS C 311 ASN C 449 HIS C 477 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.062418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.052980 restraints weight = 268852.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.053763 restraints weight = 198168.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.053851 restraints weight = 140752.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.053993 restraints weight = 137520.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.054072 restraints weight = 120618.683| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 24833 Z= 0.253 Angle : 0.716 9.799 34020 Z= 0.377 Chirality : 0.047 0.231 4081 Planarity : 0.005 0.059 4349 Dihedral : 5.810 50.158 3886 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.23 % Allowed : 4.46 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.14), residues: 3349 helix: 0.47 (0.16), residues: 1036 sheet: -0.64 (0.20), residues: 689 loop : -1.28 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 439 TYR 0.022 0.002 TYR F 72 PHE 0.033 0.003 PHE A 533 TRP 0.050 0.002 TRP A 315 HIS 0.012 0.002 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00545 (24801) covalent geometry : angle 0.70968 (33940) SS BOND : bond 0.01510 ( 16) SS BOND : angle 1.33630 ( 32) hydrogen bonds : bond 0.04931 ( 1033) hydrogen bonds : angle 6.14936 ( 2964) link_BETA1-4 : bond 0.00751 ( 7) link_BETA1-4 : angle 2.16033 ( 21) link_NAG-ASN : bond 0.00791 ( 9) link_NAG-ASN : angle 2.59371 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 189 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.1689 (ppp) cc_final: 0.0172 (ttt) REVERT: D 132 MET cc_start: 0.7673 (ptp) cc_final: 0.7462 (pmm) REVERT: D 468 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8662 (mp) REVERT: D 503 MET cc_start: 0.9270 (mmm) cc_final: 0.8908 (tpp) REVERT: D 769 ASP cc_start: 0.8503 (t0) cc_final: 0.8217 (t0) REVERT: A 177 GLN cc_start: 0.8661 (tt0) cc_final: 0.8330 (pp30) REVERT: A 181 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8495 (tm-30) REVERT: A 501 MET cc_start: 0.6690 (mtm) cc_final: 0.6322 (mtm) REVERT: A 742 GLN cc_start: 0.7289 (mm-40) cc_final: 0.6888 (mt0) REVERT: A 793 VAL cc_start: 0.7998 (t) cc_final: 0.7784 (t) REVERT: B 90 MET cc_start: 0.8143 (ttm) cc_final: 0.7880 (ttm) REVERT: B 112 MET cc_start: 0.7736 (mmm) cc_final: 0.7534 (mmt) REVERT: B 133 MET cc_start: 0.8202 (ppp) cc_final: 0.7862 (ppp) REVERT: B 782 PHE cc_start: 0.9356 (m-10) cc_final: 0.8864 (m-80) REVERT: C 326 MET cc_start: 0.5975 (mmm) cc_final: 0.5767 (mmm) REVERT: C 501 MET cc_start: 0.6002 (mtm) cc_final: 0.4966 (ptp) REVERT: C 512 MET cc_start: 0.8144 (ttm) cc_final: 0.7847 (ttp) REVERT: I 115 GLN cc_start: 0.8734 (tm-30) cc_final: 0.7828 (tm-30) outliers start: 5 outliers final: 2 residues processed: 193 average time/residue: 0.1404 time to fit residues: 46.7752 Evaluate side-chains 154 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 241 optimal weight: 1.9990 chunk 120 optimal weight: 30.0000 chunk 102 optimal weight: 0.0070 chunk 209 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 331 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 327 optimal weight: 30.0000 overall best weight: 5.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 HIS ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.060306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.051213 restraints weight = 273212.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.051446 restraints weight = 201003.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.051497 restraints weight = 180596.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.051602 restraints weight = 165831.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.051722 restraints weight = 143541.191| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 24833 Z= 0.257 Angle : 0.721 11.384 34020 Z= 0.386 Chirality : 0.047 0.235 4081 Planarity : 0.005 0.067 4349 Dihedral : 5.871 42.045 3886 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.24 % Favored : 93.73 % Rotamer: Outliers : 0.45 % Allowed : 6.09 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3349 helix: 0.09 (0.16), residues: 1030 sheet: -0.96 (0.20), residues: 690 loop : -1.50 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 774 TYR 0.021 0.002 TYR D 231 PHE 0.035 0.003 PHE A 533 TRP 0.035 0.002 TRP B 255 HIS 0.011 0.002 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00559 (24801) covalent geometry : angle 0.71638 (33940) SS BOND : bond 0.00756 ( 16) SS BOND : angle 1.46619 ( 32) hydrogen bonds : bond 0.05076 ( 1033) hydrogen bonds : angle 6.12859 ( 2964) link_BETA1-4 : bond 0.00420 ( 7) link_BETA1-4 : angle 1.89029 ( 21) link_NAG-ASN : bond 0.00723 ( 9) link_NAG-ASN : angle 2.04924 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.2285 (ppp) cc_final: 0.0850 (ttt) REVERT: D 134 MET cc_start: 0.4293 (mtp) cc_final: 0.4045 (mtp) REVERT: D 503 MET cc_start: 0.9254 (mmm) cc_final: 0.8977 (tpp) REVERT: D 777 ASP cc_start: 0.8209 (p0) cc_final: 0.7407 (m-30) REVERT: A 154 MET cc_start: 0.9160 (mmp) cc_final: 0.8932 (mmm) REVERT: A 158 TYR cc_start: 0.8017 (m-80) cc_final: 0.7791 (m-10) REVERT: A 177 GLN cc_start: 0.8732 (tt0) cc_final: 0.8298 (pp30) REVERT: A 354 MET cc_start: 0.8652 (mmm) cc_final: 0.7930 (mmp) REVERT: A 501 MET cc_start: 0.7045 (mtm) cc_final: 0.6789 (mtm) REVERT: A 742 GLN cc_start: 0.7516 (mm-40) cc_final: 0.6918 (mt0) REVERT: A 793 VAL cc_start: 0.7997 (t) cc_final: 0.7273 (t) REVERT: G 24 MET cc_start: 0.6546 (ptp) cc_final: 0.6162 (ptp) REVERT: B 133 MET cc_start: 0.7937 (ppp) cc_final: 0.7587 (ppp) REVERT: B 158 MET cc_start: 0.8429 (mtp) cc_final: 0.8160 (mtp) REVERT: B 163 GLN cc_start: 0.8445 (tt0) cc_final: 0.7884 (tp-100) REVERT: B 229 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7581 (mm) REVERT: B 782 PHE cc_start: 0.9353 (m-10) cc_final: 0.8883 (m-80) REVERT: B 788 MET cc_start: 0.6349 (mtp) cc_final: 0.6070 (mtp) REVERT: C 196 GLN cc_start: 0.7141 (tp40) cc_final: 0.6856 (tp40) REVERT: C 326 MET cc_start: 0.5832 (mmm) cc_final: 0.5621 (mmm) REVERT: C 501 MET cc_start: 0.5948 (mtm) cc_final: 0.5017 (ptp) REVERT: C 768 TRP cc_start: 0.8367 (m100) cc_final: 0.8093 (m100) REVERT: C 785 MET cc_start: 0.7199 (mmm) cc_final: 0.6489 (mmm) REVERT: I 24 MET cc_start: 0.8070 (ttm) cc_final: 0.7350 (ttp) outliers start: 10 outliers final: 4 residues processed: 183 average time/residue: 0.1366 time to fit residues: 43.6521 Evaluate side-chains 156 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 321 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 169 optimal weight: 0.0370 chunk 151 optimal weight: 0.0470 chunk 17 optimal weight: 30.0000 chunk 324 optimal weight: 10.0000 chunk 290 optimal weight: 0.0970 chunk 279 optimal weight: 40.0000 chunk 22 optimal weight: 0.6980 chunk 160 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 overall best weight: 0.9756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 359 HIS D 698 ASN A 73 GLN A 161 ASN A 293 HIS A 358 ASN A 405 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.062149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.052646 restraints weight = 267321.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.053327 restraints weight = 201002.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.053537 restraints weight = 142758.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.053662 restraints weight = 132870.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.053746 restraints weight = 118017.723| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 24833 Z= 0.107 Angle : 0.533 9.690 34020 Z= 0.280 Chirality : 0.043 0.162 4081 Planarity : 0.004 0.076 4349 Dihedral : 4.944 36.459 3886 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.09 % Allowed : 2.12 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.15), residues: 3349 helix: 0.77 (0.16), residues: 1043 sheet: -0.62 (0.20), residues: 683 loop : -1.26 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 124 TYR 0.022 0.001 TYR D 179 PHE 0.010 0.001 PHE B 186 TRP 0.048 0.001 TRP A 315 HIS 0.004 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00228 (24801) covalent geometry : angle 0.52999 (33940) SS BOND : bond 0.00525 ( 16) SS BOND : angle 1.14484 ( 32) hydrogen bonds : bond 0.03268 ( 1033) hydrogen bonds : angle 5.29438 ( 2964) link_BETA1-4 : bond 0.00338 ( 7) link_BETA1-4 : angle 1.35211 ( 21) link_NAG-ASN : bond 0.00183 ( 9) link_NAG-ASN : angle 1.49611 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.2122 (ppp) cc_final: 0.1217 (ttt) REVERT: D 134 MET cc_start: 0.4136 (mtp) cc_final: 0.3878 (mtp) REVERT: D 184 ASN cc_start: 0.8269 (m110) cc_final: 0.8067 (m110) REVERT: D 503 MET cc_start: 0.9212 (mmm) cc_final: 0.8827 (tpp) REVERT: D 769 ASP cc_start: 0.8325 (t0) cc_final: 0.8098 (t0) REVERT: D 777 ASP cc_start: 0.8046 (p0) cc_final: 0.7601 (m-30) REVERT: A 154 MET cc_start: 0.9131 (mmp) cc_final: 0.8863 (mmm) REVERT: A 155 MET cc_start: 0.9142 (ttm) cc_final: 0.8898 (ttm) REVERT: A 177 GLN cc_start: 0.8616 (tt0) cc_final: 0.8305 (pp30) REVERT: A 354 MET cc_start: 0.8668 (mmm) cc_final: 0.8219 (mmp) REVERT: A 742 GLN cc_start: 0.7361 (mm-40) cc_final: 0.7010 (mt0) REVERT: A 789 ASP cc_start: 0.9044 (m-30) cc_final: 0.8806 (t70) REVERT: A 793 VAL cc_start: 0.7981 (t) cc_final: 0.7719 (t) REVERT: B 72 LEU cc_start: 0.8138 (mt) cc_final: 0.7692 (tp) REVERT: B 133 MET cc_start: 0.7781 (ppp) cc_final: 0.7484 (ppp) REVERT: B 782 PHE cc_start: 0.9257 (m-10) cc_final: 0.8761 (m-80) REVERT: C 196 GLN cc_start: 0.6678 (tp40) cc_final: 0.6266 (tp40) REVERT: C 209 MET cc_start: 0.8366 (tpt) cc_final: 0.7911 (mmm) REVERT: C 354 MET cc_start: 0.4972 (mmm) cc_final: 0.4768 (mmm) REVERT: C 501 MET cc_start: 0.5396 (mtm) cc_final: 0.4859 (ptp) REVERT: C 762 MET cc_start: 0.6601 (mtp) cc_final: 0.6358 (mtp) REVERT: C 785 MET cc_start: 0.7143 (mmm) cc_final: 0.6567 (mmm) REVERT: I 24 MET cc_start: 0.8244 (ttm) cc_final: 0.7480 (ttm) outliers start: 2 outliers final: 0 residues processed: 184 average time/residue: 0.1267 time to fit residues: 40.3005 Evaluate side-chains 153 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 293 optimal weight: 2.9990 chunk 337 optimal weight: 50.0000 chunk 147 optimal weight: 30.0000 chunk 100 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 166 optimal weight: 0.9990 chunk 49 optimal weight: 40.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN D 698 ASN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN C 162 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.060203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.051080 restraints weight = 270725.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.051247 restraints weight = 197441.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.051615 restraints weight = 169543.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.051676 restraints weight = 133974.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.051757 restraints weight = 125735.350| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24833 Z= 0.208 Angle : 0.643 9.723 34020 Z= 0.343 Chirality : 0.045 0.199 4081 Planarity : 0.004 0.063 4349 Dihedral : 5.376 37.497 3886 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.05 % Allowed : 2.80 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.15), residues: 3349 helix: 0.46 (0.16), residues: 1042 sheet: -0.69 (0.21), residues: 645 loop : -1.40 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 233 TYR 0.018 0.002 TYR D 762 PHE 0.033 0.002 PHE G 97 TRP 0.021 0.002 TRP C 768 HIS 0.014 0.002 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00461 (24801) covalent geometry : angle 0.63845 (33940) SS BOND : bond 0.00570 ( 16) SS BOND : angle 1.40391 ( 32) hydrogen bonds : bond 0.04195 ( 1033) hydrogen bonds : angle 5.69579 ( 2964) link_BETA1-4 : bond 0.00389 ( 7) link_BETA1-4 : angle 1.66623 ( 21) link_NAG-ASN : bond 0.00663 ( 9) link_NAG-ASN : angle 2.10776 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.2821 (ppp) cc_final: 0.1571 (ttt) REVERT: D 503 MET cc_start: 0.9210 (mmm) cc_final: 0.8939 (tpp) REVERT: D 769 ASP cc_start: 0.8617 (t0) cc_final: 0.8354 (t0) REVERT: D 777 ASP cc_start: 0.8034 (p0) cc_final: 0.7299 (m-30) REVERT: A 155 MET cc_start: 0.9165 (ttm) cc_final: 0.8937 (ttm) REVERT: A 177 GLN cc_start: 0.8780 (tt0) cc_final: 0.8209 (pp30) REVERT: A 181 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8784 (tm-30) REVERT: A 793 VAL cc_start: 0.7938 (t) cc_final: 0.7651 (t) REVERT: B 133 MET cc_start: 0.7672 (ppp) cc_final: 0.7268 (ppp) REVERT: B 782 PHE cc_start: 0.9332 (m-10) cc_final: 0.8811 (m-80) REVERT: C 125 MET cc_start: 0.7899 (mpp) cc_final: 0.6948 (mpp) REVERT: C 196 GLN cc_start: 0.7173 (tp40) cc_final: 0.6861 (tp40) REVERT: C 501 MET cc_start: 0.5612 (mtm) cc_final: 0.5014 (ptp) REVERT: C 785 MET cc_start: 0.7434 (mmm) cc_final: 0.6905 (mmm) REVERT: I 24 MET cc_start: 0.7982 (ttm) cc_final: 0.7277 (ttm) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.1318 time to fit residues: 38.2526 Evaluate side-chains 143 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 77 optimal weight: 7.9990 chunk 265 optimal weight: 20.0000 chunk 291 optimal weight: 5.9990 chunk 141 optimal weight: 0.4980 chunk 131 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 222 optimal weight: 0.7980 chunk 277 optimal weight: 2.9990 chunk 127 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN D 153 GLN A 146 HIS A 161 ASN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.060560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.050611 restraints weight = 266262.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.050888 restraints weight = 194114.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.051008 restraints weight = 161019.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.051203 restraints weight = 146424.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.051354 restraints weight = 129638.948| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24833 Z= 0.162 Angle : 0.580 9.813 34020 Z= 0.308 Chirality : 0.044 0.225 4081 Planarity : 0.004 0.060 4349 Dihedral : 5.190 35.331 3886 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.05 % Allowed : 2.07 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.15), residues: 3349 helix: 0.64 (0.16), residues: 1036 sheet: -0.79 (0.21), residues: 658 loop : -1.32 (0.16), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 448 TYR 0.026 0.002 TYR A 795 PHE 0.018 0.002 PHE B 756 TRP 0.020 0.001 TRP A 315 HIS 0.007 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00359 (24801) covalent geometry : angle 0.57628 (33940) SS BOND : bond 0.00557 ( 16) SS BOND : angle 1.13551 ( 32) hydrogen bonds : bond 0.03641 ( 1033) hydrogen bonds : angle 5.46537 ( 2964) link_BETA1-4 : bond 0.00232 ( 7) link_BETA1-4 : angle 1.38815 ( 21) link_NAG-ASN : bond 0.00394 ( 9) link_NAG-ASN : angle 1.69518 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.1752 (ppp) cc_final: 0.1003 (ttt) REVERT: D 503 MET cc_start: 0.9329 (mmm) cc_final: 0.9081 (tpp) REVERT: D 769 ASP cc_start: 0.8712 (t0) cc_final: 0.8500 (t0) REVERT: D 777 ASP cc_start: 0.8133 (p0) cc_final: 0.7387 (m-30) REVERT: A 155 MET cc_start: 0.9204 (ttm) cc_final: 0.8963 (ttm) REVERT: A 177 GLN cc_start: 0.8789 (tt0) cc_final: 0.8257 (pp30) REVERT: A 181 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8764 (tm-30) REVERT: A 793 VAL cc_start: 0.8115 (t) cc_final: 0.7847 (t) REVERT: B 112 MET cc_start: 0.6553 (mmt) cc_final: 0.5934 (mmp) REVERT: B 133 MET cc_start: 0.7736 (ppp) cc_final: 0.7256 (ppp) REVERT: B 158 MET cc_start: 0.8536 (mtp) cc_final: 0.8255 (mtp) REVERT: B 782 PHE cc_start: 0.9367 (m-10) cc_final: 0.8845 (m-80) REVERT: C 196 GLN cc_start: 0.6983 (tp40) cc_final: 0.6676 (tp40) REVERT: C 501 MET cc_start: 0.5448 (mtm) cc_final: 0.5091 (ptp) REVERT: C 785 MET cc_start: 0.7408 (mmm) cc_final: 0.6749 (mmm) REVERT: I 24 MET cc_start: 0.8158 (ttm) cc_final: 0.7486 (ttt) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.1313 time to fit residues: 37.9138 Evaluate side-chains 149 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 226 optimal weight: 1.9990 chunk 282 optimal weight: 0.8980 chunk 211 optimal weight: 30.0000 chunk 321 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.060272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.051280 restraints weight = 270478.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.051497 restraints weight = 201286.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.051516 restraints weight = 175346.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.051644 restraints weight = 162687.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.051840 restraints weight = 141237.378| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24833 Z= 0.151 Angle : 0.567 8.192 34020 Z= 0.302 Chirality : 0.043 0.174 4081 Planarity : 0.004 0.060 4349 Dihedral : 5.036 34.138 3886 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.15), residues: 3349 helix: 0.77 (0.16), residues: 1045 sheet: -0.74 (0.21), residues: 651 loop : -1.34 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 448 TYR 0.014 0.002 TYR C 88 PHE 0.017 0.002 PHE G 97 TRP 0.022 0.001 TRP A 315 HIS 0.006 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00334 (24801) covalent geometry : angle 0.56355 (33940) SS BOND : bond 0.00438 ( 16) SS BOND : angle 0.96868 ( 32) hydrogen bonds : bond 0.03478 ( 1033) hydrogen bonds : angle 5.32743 ( 2964) link_BETA1-4 : bond 0.00221 ( 7) link_BETA1-4 : angle 1.35981 ( 21) link_NAG-ASN : bond 0.00421 ( 9) link_NAG-ASN : angle 1.67427 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.2467 (ppp) cc_final: 0.1440 (ttt) REVERT: D 142 MET cc_start: 0.7752 (pmm) cc_final: 0.7450 (pmm) REVERT: D 503 MET cc_start: 0.9175 (mmm) cc_final: 0.8821 (tpp) REVERT: D 777 ASP cc_start: 0.8369 (p0) cc_final: 0.7448 (m-30) REVERT: A 155 MET cc_start: 0.9183 (ttm) cc_final: 0.8975 (ttm) REVERT: A 177 GLN cc_start: 0.8786 (tt0) cc_final: 0.8321 (pp30) REVERT: A 181 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8769 (tm-30) REVERT: A 793 VAL cc_start: 0.8046 (t) cc_final: 0.7576 (t) REVERT: B 112 MET cc_start: 0.7370 (mmt) cc_final: 0.6687 (mmp) REVERT: B 133 MET cc_start: 0.7277 (ppp) cc_final: 0.6949 (ppp) REVERT: B 705 MET cc_start: 0.5421 (tpt) cc_final: 0.5207 (tpt) REVERT: B 782 PHE cc_start: 0.9342 (m-10) cc_final: 0.8826 (m-80) REVERT: C 125 MET cc_start: 0.7665 (mpp) cc_final: 0.7419 (mpp) REVERT: C 196 GLN cc_start: 0.7123 (tp40) cc_final: 0.6766 (tp40) REVERT: C 209 MET cc_start: 0.8316 (tpt) cc_final: 0.7860 (mmm) REVERT: C 501 MET cc_start: 0.5545 (mtm) cc_final: 0.5194 (ptp) REVERT: C 785 MET cc_start: 0.7401 (mmm) cc_final: 0.6637 (mmm) REVERT: J 126 GLU cc_start: 0.6449 (pm20) cc_final: 0.6174 (pp20) REVERT: I 24 MET cc_start: 0.8225 (ttm) cc_final: 0.7870 (ttm) REVERT: I 115 GLN cc_start: 0.8551 (tm-30) cc_final: 0.7960 (tp40) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1366 time to fit residues: 40.3792 Evaluate side-chains 148 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 81 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 242 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 288 optimal weight: 8.9990 chunk 184 optimal weight: 5.9990 chunk 283 optimal weight: 50.0000 chunk 103 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 218 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 HIS D 153 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 HIS ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.061310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.051560 restraints weight = 265529.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.052718 restraints weight = 192202.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.053029 restraints weight = 125520.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.053125 restraints weight = 101266.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.053147 restraints weight = 101941.184| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24833 Z= 0.113 Angle : 0.528 9.046 34020 Z= 0.277 Chirality : 0.043 0.185 4081 Planarity : 0.004 0.057 4349 Dihedral : 4.769 33.168 3886 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.66 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.15), residues: 3349 helix: 1.03 (0.16), residues: 1039 sheet: -0.67 (0.21), residues: 661 loop : -1.26 (0.16), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 763 TYR 0.026 0.001 TYR D 179 PHE 0.016 0.001 PHE B 756 TRP 0.019 0.001 TRP A 315 HIS 0.009 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00250 (24801) covalent geometry : angle 0.52490 (33940) SS BOND : bond 0.00378 ( 16) SS BOND : angle 0.95731 ( 32) hydrogen bonds : bond 0.03097 ( 1033) hydrogen bonds : angle 5.06960 ( 2964) link_BETA1-4 : bond 0.00276 ( 7) link_BETA1-4 : angle 1.26823 ( 21) link_NAG-ASN : bond 0.00220 ( 9) link_NAG-ASN : angle 1.41669 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.2380 (ppp) cc_final: 0.1308 (ttt) REVERT: D 142 MET cc_start: 0.7676 (pmm) cc_final: 0.7012 (pmm) REVERT: D 503 MET cc_start: 0.9320 (mmm) cc_final: 0.8999 (tpp) REVERT: D 777 ASP cc_start: 0.8247 (p0) cc_final: 0.7294 (m-30) REVERT: A 155 MET cc_start: 0.9194 (ttm) cc_final: 0.8981 (ttm) REVERT: A 177 GLN cc_start: 0.8740 (tt0) cc_final: 0.8211 (pp30) REVERT: A 181 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8728 (tm-30) REVERT: A 209 MET cc_start: 0.8176 (mmm) cc_final: 0.7917 (mmp) REVERT: A 240 MET cc_start: 0.7807 (mmt) cc_final: 0.7313 (mmt) REVERT: A 793 VAL cc_start: 0.8063 (t) cc_final: 0.7842 (t) REVERT: B 90 MET cc_start: 0.8552 (tmm) cc_final: 0.8158 (tmm) REVERT: B 112 MET cc_start: 0.5968 (mmt) cc_final: 0.5443 (mmp) REVERT: B 133 MET cc_start: 0.7323 (ppp) cc_final: 0.6710 (ppp) REVERT: B 782 PHE cc_start: 0.9318 (m-10) cc_final: 0.8827 (m-80) REVERT: C 125 MET cc_start: 0.7531 (mpp) cc_final: 0.7228 (mpp) REVERT: C 196 GLN cc_start: 0.6964 (tp40) cc_final: 0.6555 (tp40) REVERT: C 209 MET cc_start: 0.8429 (tpt) cc_final: 0.7999 (mmm) REVERT: C 785 MET cc_start: 0.7340 (mmm) cc_final: 0.6595 (mmm) REVERT: I 24 MET cc_start: 0.8139 (ttm) cc_final: 0.7604 (ttt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1338 time to fit residues: 39.5158 Evaluate side-chains 151 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 49 optimal weight: 30.0000 chunk 31 optimal weight: 30.0000 chunk 218 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 288 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 262 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.061136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.052087 restraints weight = 269717.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.052483 restraints weight = 187809.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.052742 restraints weight = 149406.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.052832 restraints weight = 128072.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.052926 restraints weight = 115891.979| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24833 Z= 0.122 Angle : 0.532 8.346 34020 Z= 0.280 Chirality : 0.043 0.165 4081 Planarity : 0.004 0.056 4349 Dihedral : 4.668 32.463 3886 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3349 helix: 1.07 (0.16), residues: 1036 sheet: -0.61 (0.21), residues: 636 loop : -1.30 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 763 TYR 0.013 0.001 TYR D 762 PHE 0.016 0.001 PHE B 756 TRP 0.018 0.001 TRP A 315 HIS 0.008 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00273 (24801) covalent geometry : angle 0.52957 (33940) SS BOND : bond 0.00389 ( 16) SS BOND : angle 0.94884 ( 32) hydrogen bonds : bond 0.03158 ( 1033) hydrogen bonds : angle 5.05658 ( 2964) link_BETA1-4 : bond 0.00225 ( 7) link_BETA1-4 : angle 1.32359 ( 21) link_NAG-ASN : bond 0.00293 ( 9) link_NAG-ASN : angle 1.46856 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.2959 (ppp) cc_final: 0.1989 (ttt) REVERT: D 142 MET cc_start: 0.7678 (pmm) cc_final: 0.7444 (pmm) REVERT: D 503 MET cc_start: 0.9241 (mmm) cc_final: 0.8920 (tpp) REVERT: D 777 ASP cc_start: 0.8361 (p0) cc_final: 0.7318 (m-30) REVERT: A 177 GLN cc_start: 0.8761 (tt0) cc_final: 0.8247 (pp30) REVERT: A 240 MET cc_start: 0.7834 (mmt) cc_final: 0.7327 (mmt) REVERT: A 706 MET cc_start: 0.8232 (ptp) cc_final: 0.7574 (ptp) REVERT: A 793 VAL cc_start: 0.8045 (t) cc_final: 0.7599 (t) REVERT: B 90 MET cc_start: 0.8442 (tmm) cc_final: 0.7983 (tmm) REVERT: B 112 MET cc_start: 0.6338 (mmt) cc_final: 0.5708 (mmp) REVERT: B 133 MET cc_start: 0.7302 (ppp) cc_final: 0.6788 (ppp) REVERT: B 705 MET cc_start: 0.5840 (tpt) cc_final: 0.5618 (tpt) REVERT: B 782 PHE cc_start: 0.9448 (m-10) cc_final: 0.9037 (m-80) REVERT: C 125 MET cc_start: 0.7564 (mpp) cc_final: 0.7305 (mpp) REVERT: C 196 GLN cc_start: 0.6897 (tp40) cc_final: 0.6528 (tp40) REVERT: C 209 MET cc_start: 0.8392 (tpt) cc_final: 0.7979 (mmm) REVERT: C 785 MET cc_start: 0.7353 (mmm) cc_final: 0.6613 (mmm) REVERT: I 24 MET cc_start: 0.8249 (ttm) cc_final: 0.7773 (ttt) REVERT: I 115 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8059 (tp-100) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1353 time to fit residues: 40.0775 Evaluate side-chains 149 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 187 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 322 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 310 optimal weight: 8.9990 chunk 222 optimal weight: 0.4980 chunk 252 optimal weight: 6.9990 chunk 308 optimal weight: 7.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN A 28 ASN ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.058754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.049812 restraints weight = 274443.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.049912 restraints weight = 207883.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.050103 restraints weight = 181397.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.050139 restraints weight = 162754.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.050293 restraints weight = 143969.609| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 24833 Z= 0.253 Angle : 0.718 9.697 34020 Z= 0.381 Chirality : 0.046 0.192 4081 Planarity : 0.005 0.070 4349 Dihedral : 5.666 34.664 3886 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.73 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.15), residues: 3349 helix: 0.38 (0.16), residues: 1034 sheet: -1.01 (0.20), residues: 636 loop : -1.51 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 763 TYR 0.029 0.002 TYR D 179 PHE 0.022 0.003 PHE A 137 TRP 0.028 0.002 TRP C 768 HIS 0.012 0.002 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00556 (24801) covalent geometry : angle 0.71296 (33940) SS BOND : bond 0.00621 ( 16) SS BOND : angle 1.48326 ( 32) hydrogen bonds : bond 0.04446 ( 1033) hydrogen bonds : angle 5.81888 ( 2964) link_BETA1-4 : bond 0.00429 ( 7) link_BETA1-4 : angle 1.75254 ( 21) link_NAG-ASN : bond 0.00883 ( 9) link_NAG-ASN : angle 2.29438 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.3272 (ppp) cc_final: 0.2541 (ttt) REVERT: D 142 MET cc_start: 0.7934 (pmm) cc_final: 0.7262 (pmm) REVERT: D 503 MET cc_start: 0.9166 (mmm) cc_final: 0.8882 (tpp) REVERT: D 777 ASP cc_start: 0.8346 (p0) cc_final: 0.7410 (m-30) REVERT: A 155 MET cc_start: 0.9226 (ttm) cc_final: 0.8987 (ttm) REVERT: A 161 ASN cc_start: 0.8468 (t0) cc_final: 0.7836 (p0) REVERT: A 177 GLN cc_start: 0.8866 (tt0) cc_final: 0.8381 (pp30) REVERT: A 181 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8865 (tm-30) REVERT: A 209 MET cc_start: 0.8005 (mmm) cc_final: 0.7714 (mmp) REVERT: A 793 VAL cc_start: 0.8077 (t) cc_final: 0.7393 (t) REVERT: B 90 MET cc_start: 0.8612 (tmm) cc_final: 0.8176 (tmm) REVERT: B 112 MET cc_start: 0.7435 (mmt) cc_final: 0.7078 (mmp) REVERT: B 133 MET cc_start: 0.7418 (ppp) cc_final: 0.6852 (ppp) REVERT: B 782 PHE cc_start: 0.9505 (m-10) cc_final: 0.9013 (m-80) REVERT: C 125 MET cc_start: 0.8178 (mpp) cc_final: 0.7967 (mpp) REVERT: C 785 MET cc_start: 0.7573 (mmm) cc_final: 0.6563 (mmm) REVERT: J 126 GLU cc_start: 0.6534 (pp20) cc_final: 0.6039 (pp20) REVERT: I 24 MET cc_start: 0.8347 (ttm) cc_final: 0.7711 (ttt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1333 time to fit residues: 38.1911 Evaluate side-chains 139 residues out of total 2953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 308 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.059943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.050798 restraints weight = 269653.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.051173 restraints weight = 195571.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.051306 restraints weight = 159707.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.051399 restraints weight = 143520.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.051550 restraints weight = 127276.263| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24833 Z= 0.129 Angle : 0.564 8.021 34020 Z= 0.297 Chirality : 0.043 0.190 4081 Planarity : 0.004 0.062 4349 Dihedral : 5.093 33.625 3886 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.15), residues: 3349 helix: 0.84 (0.16), residues: 1033 sheet: -0.88 (0.21), residues: 630 loop : -1.40 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 763 TYR 0.026 0.001 TYR D 179 PHE 0.016 0.001 PHE B 756 TRP 0.030 0.001 TRP A 315 HIS 0.007 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00288 (24801) covalent geometry : angle 0.56094 (33940) SS BOND : bond 0.00400 ( 16) SS BOND : angle 1.01471 ( 32) hydrogen bonds : bond 0.03402 ( 1033) hydrogen bonds : angle 5.30477 ( 2964) link_BETA1-4 : bond 0.00251 ( 7) link_BETA1-4 : angle 1.32614 ( 21) link_NAG-ASN : bond 0.00308 ( 9) link_NAG-ASN : angle 1.47896 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4851.97 seconds wall clock time: 84 minutes 10.88 seconds (5050.88 seconds total)