Starting phenix.real_space_refine on Mon Feb 19 05:39:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sab_24947/02_2024/7sab_24947_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sab_24947/02_2024/7sab_24947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sab_24947/02_2024/7sab_24947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sab_24947/02_2024/7sab_24947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sab_24947/02_2024/7sab_24947_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sab_24947/02_2024/7sab_24947_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.441 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 298 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 15083 2.51 5 N 3828 2.21 5 O 4471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 213": "OE1" <-> "OE2" Residue "A TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 528": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23510 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5913 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 228 Chain: "B" Number of atoms: 5760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5760 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 456 Unresolved non-hydrogen angles: 542 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 10, 'TYR:plan': 7, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 24, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 281 Chain: "C" Number of atoms: 5896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5896 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 396 Unresolved non-hydrogen angles: 459 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 234 Chain: "D" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5755 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 464 Unresolved non-hydrogen angles: 556 Unresolved non-hydrogen dihedrals: 410 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'TYR:plan': 8, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 24, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 298 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "B" 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: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'1PC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" 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 Time building chain proxies: 12.55, per 1000 atoms: 0.53 Number of scatterers: 23510 At special positions: 0 Unit cell: (123.264, 154.08, 183.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 4471 8.00 N 3828 7.00 C 15083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.04 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 A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.04 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 C 744 " - pdb=" SG CYS C 798 " distance=2.03 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=2.52 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 901 " - " ASN B 491 " " NAG C 901 " - " ASN C 203 " " NAG D 901 " - " ASN D 491 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN D 688 " Time building additional restraints: 9.49 Conformation dependent library (CDL) restraints added in 4.4 seconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5904 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 29 sheets defined 38.9% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.09 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 removed outlier: 3.872A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 85 removed outlier: 4.599A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 112 removed outlier: 3.675A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 144 through 157 removed outlier: 4.680A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 removed outlier: 3.749A pdb=" N GLU A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.866A pdb=" N MET A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.995A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.967A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 277 through 296 removed outlier: 3.772A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 325 removed outlier: 3.651A pdb=" N LEU A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 459 through 469 removed outlier: 3.947A pdb=" N THR A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.662A pdb=" N GLU A 504 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 581 removed outlier: 3.573A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 579 " --> pdb=" O VAL A 575 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 580 " --> pdb=" O MET A 576 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.691A pdb=" N SER A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 612 " --> pdb=" O TRP A 608 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 655 removed outlier: 3.537A pdb=" N ILE A 631 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 640 " --> pdb=" O TRP A 636 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 673 No H-bonds generated for 'chain 'A' and resid 670 through 673' Processing helix chain 'A' and resid 688 through 695 removed outlier: 3.529A pdb=" N TYR A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 709 removed outlier: 4.459A pdb=" N THR A 701 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG A 704 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A 705 " --> pdb=" O MET A 702 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 708 " --> pdb=" O HIS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 722 removed outlier: 3.966A pdb=" N ARG A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.770A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 742 " --> pdb=" O PHE A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 782 removed outlier: 3.576A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS A 780 " --> pdb=" O ILE A 776 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 792 removed outlier: 3.542A pdb=" N LEU A 788 " --> pdb=" O PHE A 784 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 826 removed outlier: 4.638A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 824 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 839 Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 107 through 118 Processing helix chain 'B' and resid 128 through 131 Processing helix chain 'B' and resid 150 through 163 Processing helix chain 'B' and resid 179 through 192 removed outlier: 3.670A pdb=" N ILE B 190 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU B 191 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN B 192 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 234 through 247 removed outlier: 3.506A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 290 through 311 removed outlier: 3.814A pdb=" N SER B 309 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 329 removed outlier: 3.939A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 329' Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.795A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 333 through 339' Processing helix chain 'B' and resid 461 through 471 Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 517 through 520 No H-bonds generated for 'chain 'B' and resid 517 through 520' Processing helix chain 'B' and resid 549 through 552 No H-bonds generated for 'chain 'B' and resid 549 through 552' Processing helix chain 'B' and resid 558 through 578 removed outlier: 4.096A pdb=" N GLU B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 612 Processing helix chain 'B' and resid 626 through 654 removed outlier: 3.693A pdb=" N PHE B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 672 No H-bonds generated for 'chain 'B' and resid 669 through 672' Processing helix chain 'B' and resid 690 through 698 removed outlier: 3.728A pdb=" N ASN B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 707 removed outlier: 4.127A pdb=" N ALA B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TYR B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET B 706 " --> pdb=" O MET B 702 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 700 through 707' Processing helix chain 'B' and resid 715 through 722 Processing helix chain 'B' and resid 734 through 742 removed outlier: 3.794A pdb=" N GLY B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 786 removed outlier: 3.595A pdb=" N ASP B 786 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 796 Processing helix chain 'B' and resid 815 through 844 removed outlier: 3.607A pdb=" N ALA B 819 " --> pdb=" O ILE B 815 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLY B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N VAL B 821 " --> pdb=" O ASN B 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 51 removed outlier: 4.004A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 85 removed outlier: 4.797A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 removed outlier: 4.837A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 144 through 158 removed outlier: 4.909A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET C 154 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 187 removed outlier: 4.175A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 213 removed outlier: 3.738A pdb=" N MET C 209 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.887A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 277 through 296 removed outlier: 3.651A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 325 removed outlier: 3.518A pdb=" N VAL C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 470 removed outlier: 3.509A pdb=" N MET C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 504 Processing helix chain 'C' and resid 553 through 556 No H-bonds generated for 'chain 'C' and resid 553 through 556' Processing helix chain 'C' and resid 560 through 581 removed outlier: 3.752A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET C 576 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU C 577 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 615 removed outlier: 3.942A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 613 " --> pdb=" O PHE C 609 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU C 615 " --> pdb=" O TRP C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 656 removed outlier: 3.940A pdb=" N ILE C 631 " --> pdb=" O PHE C 627 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 640 " --> pdb=" O TRP C 636 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA C 652 " --> pdb=" O THR C 648 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL C 656 " --> pdb=" O ALA C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 670 through 672 No H-bonds generated for 'chain 'C' and resid 670 through 672' Processing helix chain 'C' and resid 688 through 694 Processing helix chain 'C' and resid 700 through 706 removed outlier: 4.571A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 722 removed outlier: 3.679A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 742 removed outlier: 4.607A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 739 " --> pdb=" O VAL C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 781 removed outlier: 4.063A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS C 780 " --> pdb=" O ILE C 776 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 792 Processing helix chain 'C' and resid 810 through 812 No H-bonds generated for 'chain 'C' and resid 810 through 812' Processing helix chain 'C' and resid 814 through 840 removed outlier: 5.389A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU C 830 " --> pdb=" O ALA C 826 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.852A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 107 through 118 Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 150 through 163 Processing helix chain 'D' and resid 179 through 190 removed outlier: 3.679A pdb=" N THR D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 222 removed outlier: 3.974A pdb=" N LYS D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 247 removed outlier: 4.259A pdb=" N THR D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 290 through 311 removed outlier: 3.778A pdb=" N ARG D 294 " --> pdb=" O PRO D 290 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D 309 " --> pdb=" O SER D 305 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 328 removed outlier: 4.078A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 328' Processing helix chain 'D' and resid 336 through 339 No H-bonds generated for 'chain 'D' and resid 336 through 339' Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 496 through 502 Processing helix chain 'D' and resid 518 through 522 Processing helix chain 'D' and resid 549 through 552 No H-bonds generated for 'chain 'D' and resid 549 through 552' Processing helix chain 'D' and resid 558 through 577 removed outlier: 3.827A pdb=" N ALA D 571 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL D 572 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ALA D 573 " --> pdb=" O VAL D 569 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL D 574 " --> pdb=" O SER D 570 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE D 575 " --> pdb=" O ALA D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 614 removed outlier: 3.922A pdb=" N LEU D 609 " --> pdb=" O ALA D 605 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 655 Processing helix chain 'D' and resid 669 through 671 No H-bonds generated for 'chain 'D' and resid 669 through 671' Processing helix chain 'D' and resid 674 through 676 No H-bonds generated for 'chain 'D' and resid 674 through 676' Processing helix chain 'D' and resid 690 through 697 removed outlier: 3.620A pdb=" N ASN D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 708 removed outlier: 3.788A pdb=" N GLY D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LYS D 708 " --> pdb=" O ALA D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 722 Processing helix chain 'D' and resid 733 through 741 removed outlier: 4.244A pdb=" N GLY D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 786 removed outlier: 3.939A pdb=" N LEU D 781 " --> pdb=" O ASP D 777 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN D 782 " --> pdb=" O LEU D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 796 Processing helix chain 'D' and resid 815 through 844 removed outlier: 5.532A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 59 through 66 Processing sheet with id= B, first strand: chain 'A' and resid 193 through 197 removed outlier: 4.014A pdb=" N LEU A 165 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 195 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 167 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 222 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER A 168 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 267 through 271 removed outlier: 3.520A pdb=" N GLY A 268 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS A 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 398 through 402 removed outlier: 3.607A pdb=" N GLU A 475 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE A 400 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 402 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.656A pdb=" N VAL A 451 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 487 through 489 removed outlier: 3.886A pdb=" N GLU A 488 " --> pdb=" O GLU A 497 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 540 through 543 removed outlier: 4.458A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 747 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 532 through 536 removed outlier: 6.966A pdb=" N PHE A 758 " --> pdb=" O PHE A 533 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR A 535 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N SER A 756 " --> pdb=" O TYR A 535 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 36 through 41 removed outlier: 6.235A pdb=" N ARG B 67 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N VAL B 39 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU B 69 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU B 41 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 71 " --> pdb=" O LEU B 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 96 through 99 removed outlier: 8.822A pdb=" N PHE B 99 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU B 124 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 170 through 173 removed outlier: 3.524A pdb=" N TYR B 231 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR B 255 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU B 230 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 257 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 278 through 282 removed outlier: 3.541A pdb=" N SER B 279 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 407 through 409 removed outlier: 6.666A pdb=" N ASP B 477 " --> pdb=" O ILE B 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 417 through 420 removed outlier: 3.725A pdb=" N CYS B 456 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 437 through 439 removed outlier: 3.627A pdb=" N LYS B 438 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 729 through 732 removed outlier: 3.833A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 538 " --> pdb=" O VAL B 749 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 59 through 65 removed outlier: 6.385A pdb=" N ALA C 89 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N VAL C 32 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU C 91 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 92 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 164 through 167 removed outlier: 4.217A pdb=" N SER C 222 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL C 246 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU C 221 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU C 248 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 269 through 271 removed outlier: 6.343A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 366 " --> pdb=" O ILE C 373 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 397 through 401 removed outlier: 6.879A pdb=" N THR C 473 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE C 400 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU C 475 " --> pdb=" O ILE C 400 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 409 through 412 removed outlier: 3.535A pdb=" N TYR C 410 " --> pdb=" O TYR C 456 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 487 through 490 removed outlier: 3.527A pdb=" N GLU C 488 " --> pdb=" O GLU C 497 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 490 " --> pdb=" O LYS C 495 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LYS C 495 " --> pdb=" O VAL C 490 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'C' and resid 729 through 732 removed outlier: 3.911A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 542 " --> pdb=" O VAL C 747 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C 747 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 67 through 73 removed outlier: 3.545A pdb=" N ILE D 37 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU D 69 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 41 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET D 73 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY D 96 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE D 40 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL D 98 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL D 42 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA D 100 " --> pdb=" O VAL D 42 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 170 through 173 removed outlier: 6.592A pdb=" N THR D 255 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU D 230 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 257 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 278 through 282 removed outlier: 3.879A pdb=" N LEU D 362 " --> pdb=" O TRP D 379 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN D 385 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 405 through 409 removed outlier: 6.464A pdb=" N THR D 475 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE D 408 " --> pdb=" O THR D 475 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASP D 477 " --> pdb=" O ILE D 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'D' and resid 417 through 420 removed outlier: 3.540A pdb=" N CYS D 456 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 729 through 732 removed outlier: 3.725A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL D 538 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) 752 hydrogen bonds defined for protein. 2160 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: 7.50 Time building geometry restraints manager: 10.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3931 1.30 - 1.44: 6448 1.44 - 1.57: 13428 1.57 - 1.71: 1 1.71 - 1.84: 218 Bond restraints: 24026 Sorted by residual: bond pdb=" CG 1PC C 903 " pdb=" NM 1PC C 903 " ideal model delta sigma weight residual 1.461 1.212 0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" CA ASN D 616 " pdb=" C ASN D 616 " ideal model delta sigma weight residual 1.523 1.408 0.116 1.34e-02 5.57e+03 7.45e+01 bond pdb=" CA VAL D 640 " pdb=" C VAL D 640 " ideal model delta sigma weight residual 1.524 1.413 0.111 1.30e-02 5.92e+03 7.26e+01 bond pdb=" N ALA D 639 " pdb=" CA ALA D 639 " ideal model delta sigma weight residual 1.459 1.359 0.100 1.19e-02 7.06e+03 7.11e+01 bond pdb=" N PHE B 642 " pdb=" CA PHE B 642 " ideal model delta sigma weight residual 1.459 1.365 0.094 1.19e-02 7.06e+03 6.29e+01 ... (remaining 24021 not shown) Histogram of bond angle deviations from ideal: 97.75 - 106.28: 650 106.28 - 114.80: 14430 114.80 - 123.33: 16937 123.33 - 131.85: 766 131.85 - 140.37: 55 Bond angle restraints: 32838 Sorted by residual: angle pdb=" N GLU B 658 " pdb=" CA GLU B 658 " pdb=" C GLU B 658 " ideal model delta sigma weight residual 110.28 124.61 -14.33 1.48e+00 4.57e-01 9.37e+01 angle pdb=" CA PHE D 638 " pdb=" C PHE D 638 " pdb=" N ALA D 639 " ideal model delta sigma weight residual 118.01 105.57 12.44 1.30e+00 5.92e-01 9.15e+01 angle pdb=" C TYR B 175 " pdb=" N PHE B 176 " pdb=" CA PHE B 176 " ideal model delta sigma weight residual 121.80 140.37 -18.57 2.44e+00 1.68e-01 5.79e+01 angle pdb=" C ASN D 616 " pdb=" N SER D 617 " pdb=" CA SER D 617 " ideal model delta sigma weight residual 120.58 107.61 12.97 1.71e+00 3.42e-01 5.75e+01 angle pdb=" C TYR D 646 " pdb=" CA TYR D 646 " pdb=" CB TYR D 646 " ideal model delta sigma weight residual 110.79 98.98 11.81 1.66e+00 3.63e-01 5.06e+01 ... (remaining 32833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.97: 13572 24.97 - 49.94: 629 49.94 - 74.91: 43 74.91 - 99.89: 12 99.89 - 124.86: 2 Dihedral angle restraints: 14258 sinusoidal: 5109 harmonic: 9149 Sorted by residual: dihedral pdb=" CB CYS C 436 " pdb=" SG CYS C 436 " pdb=" SG CYS C 455 " pdb=" CB CYS C 455 " ideal model delta sinusoidal sigma weight residual -86.00 -169.37 83.37 1 1.00e+01 1.00e-02 8.49e+01 dihedral pdb=" CA THR A 550 " pdb=" C THR A 550 " pdb=" N LEU A 551 " pdb=" CA LEU A 551 " ideal model delta harmonic sigma weight residual 180.00 146.65 33.35 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" C ASN D 615 " pdb=" N ASN D 615 " pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " ideal model delta harmonic sigma weight residual -122.60 -138.95 16.35 0 2.50e+00 1.60e-01 4.28e+01 ... (remaining 14255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 3877 0.170 - 0.340: 22 0.340 - 0.510: 6 0.510 - 0.679: 1 0.679 - 0.849: 4 Chirality restraints: 3910 Sorted by residual: chirality pdb=" CA ASN D 615 " pdb=" N ASN D 615 " pdb=" C ASN D 615 " pdb=" CB ASN D 615 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" CA THR D 647 " pdb=" N THR D 647 " pdb=" C THR D 647 " pdb=" CB THR D 647 " both_signs ideal model delta sigma weight residual False 2.53 1.75 0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CA VAL D 640 " pdb=" N VAL D 640 " pdb=" C VAL D 640 " pdb=" CB VAL D 640 " both_signs ideal model delta sigma weight residual False 2.44 1.70 0.75 2.00e-01 2.50e+01 1.39e+01 ... (remaining 3907 not shown) Planarity restraints: 4189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 638 " 0.031 2.00e-02 2.50e+03 6.94e-02 4.82e+01 pdb=" C PHE D 638 " -0.120 2.00e-02 2.50e+03 pdb=" O PHE D 638 " 0.048 2.00e-02 2.50e+03 pdb=" N ALA D 639 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 652 " -0.034 2.00e-02 2.50e+03 6.87e-02 4.73e+01 pdb=" C ALA B 652 " 0.119 2.00e-02 2.50e+03 pdb=" O ALA B 652 " -0.045 2.00e-02 2.50e+03 pdb=" N PHE B 653 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 615 " -0.026 2.00e-02 2.50e+03 5.39e-02 2.91e+01 pdb=" C ASN D 615 " 0.093 2.00e-02 2.50e+03 pdb=" O ASN D 615 " -0.036 2.00e-02 2.50e+03 pdb=" N ASN D 616 " -0.031 2.00e-02 2.50e+03 ... (remaining 4186 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 182 2.54 - 3.13: 19542 3.13 - 3.72: 34743 3.72 - 4.31: 43195 4.31 - 4.90: 69789 Nonbonded interactions: 167451 Sorted by model distance: nonbonded pdb=" O ALA D 636 " pdb=" CB ALA D 639 " model vdw 1.955 3.460 nonbonded pdb=" O GLN D 437 " pdb=" NE2 GLN D 437 " model vdw 2.071 2.520 nonbonded pdb=" O LEU C 655 " pdb=" CG2 VAL C 656 " model vdw 2.121 3.460 nonbonded pdb=" CG1 VAL D 613 " pdb=" CE1 PHE D 614 " model vdw 2.151 3.760 nonbonded pdb=" O ALA D 648 " pdb=" C ASN D 649 " model vdw 2.170 3.270 ... (remaining 167446 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 186 or (resid 187 through 188 and (name N or na \ me CA or name C or name O or name CB )) or resid 189 through 259 or (resid 260 a \ nd (name N or name CA or name C or name O or name CB )) or resid 261 through 344 \ or (resid 345 and (name N or name CA or name C or name O or name CB )) or resid \ 346 through 482 or (resid 483 and (name N or name CA or name C or name O or nam \ e CB )) or resid 484 through 508 or (resid 509 through 510 and (name N or name C \ A or name C or name O or name CB )) or resid 511 through 542 or (resid 543 and ( \ name N or name CA or name C or name O or name CB )) or resid 544 through 657 or \ (resid 658 through 659 and (name N or name CA or name C or name O or name CB )) \ or resid 660 through 662 or (resid 663 and (name N or name CA or name C or name \ O or name CB )) or resid 664 through 693 or (resid 694 and (name N or name CA or \ name C or name O or name CB )) or resid 695 through 707 or (resid 708 and (name \ N or name CA or name C or name O or name CB )) or resid 709 through 724 or (res \ id 725 and (name N or name CA or name C or name O or name CB )) or resid 726 thr \ ough 841 or resid 901 through 902)) selection = (chain 'C' and (resid 25 through 386 or (resid 387 through 388 and (name N or na \ me CA or name C or name O or name CB )) or resid 389 through 396 or (resid 397 a \ nd (name N or name CA or name C or name O or name CB )) or resid 398 through 535 \ or (resid 536 and (name N or name CA or name C or name O or name CB )) or resid \ 537 through 629 or (resid 630 and (name N or name CA or name C or name O or nam \ e CB )) or resid 631 through 763 or (resid 764 and (name N or name CA or name C \ or name O or name CB )) or resid 765 through 817 or (resid 818 through 819 and ( \ name N or name CA or name C or name O or name CB )) or resid 820 through 828 or \ (resid 829 and (name N or name CA or name C or name O or name CB )) or resid 830 \ through 841 or resid 901 through 902)) } ncs_group { reference = (chain 'B' and (resid 34 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 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 through 66 or (resid 67 and ( \ name N or name CA or name C or name O or name CB )) or resid 68 through 178 or ( \ resid 179 and (name N or name CA or name C or name O or name CB )) or resid 180 \ through 233 or (resid 234 and (name N or name CA or name C or name O or name CB \ )) or resid 235 through 283 or (resid 284 and (name N or name CA or name C or na \ me O or name CB )) or resid 285 through 482 or (resid 483 and (name N or name CA \ or name C or name O or name CB )) or resid 484 or (resid 485 and (name N or nam \ e CA or name C or name O or name CB )) or resid 486 through 488 or (resid 489 an \ d (name N or name CA or name C or name O or name CB )) or resid 490 through 556 \ or (resid 557 and (name N or name CA or name C or name O or name CB )) or resid \ 558 through 746 or (resid 747 and (name N or name CA or name C or name O or name \ CB )) or resid 748 through 801 or (resid 802 through 807 and (name N or name CA \ or name C or name O or name CB )) or resid 808 through 835 or (resid 836 and (n \ ame N or name CA or name C or name O or name CB )) or resid 837 through 845 or r \ esid 901 through 902)) selection = (chain 'D' and (resid 34 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 197 or (resid 198 and (name N or n \ ame CA or name C or name O or name CB )) or resid 199 or (resid 200 through 201 \ and (name N or name CA or name C or name O or name CB )) or resid 202 through 20 \ 6 or (resid 207 and (name N or name CA or name C or name O or name CB )) or resi \ d 208 or (resid 209 through 211 and (name N or name CA or name C or name O or na \ me CB )) or resid 212 through 377 or (resid 378 and (name N or name CA or name C \ or name O or name CB )) or resid 379 through 487 or (resid 488 through 489 and \ (name N or name CA or name C or name O or name CB )) or resid 490 through 502 or \ (resid 503 through 504 and (name N or name CA or name C or name O or name CB )) \ or resid 505 through 560 or (resid 561 and (name N or name CA or name C or name \ O or name CB )) or resid 562 through 655 or (resid 656 through 659 and (name N \ or name CA or name C or name O or name CB )) or resid 660 through 672 or (resid \ 673 and (name N or name CA or name C or name O or name CB )) or resid 674 throug \ h 721 or (resid 722 and (name N or name CA or name C or name O or name CB )) or \ resid 723 through 772 or (resid 773 and (name N or name CA or name C or name O o \ r name CB )) or resid 774 through 844 or (resid 845 and (name N or name CA or na \ me C or name O or name CB )) or resid 901 through 902)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 3.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.040 Extract box with map and model: 15.410 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 62.450 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.249 24026 Z= 0.405 Angle : 0.808 18.574 32838 Z= 0.451 Chirality : 0.055 0.849 3910 Planarity : 0.006 0.128 4184 Dihedral : 13.431 124.857 8306 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.31 % Favored : 93.49 % Rotamer: Outliers : 0.38 % Allowed : 0.42 % Favored : 99.19 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.15), residues: 3136 helix: 0.12 (0.16), residues: 1080 sheet: -0.92 (0.29), residues: 354 loop : -1.77 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 636 HIS 0.003 0.001 HIS A 38 PHE 0.039 0.002 PHE D 642 TYR 0.042 0.001 TYR D 646 ARG 0.008 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 470 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.9008 (mtp-110) cc_final: 0.8336 (tpt90) REVERT: A 197 PHE cc_start: 0.7940 (t80) cc_final: 0.7664 (t80) REVERT: A 198 ASP cc_start: 0.8985 (p0) cc_final: 0.8364 (p0) REVERT: A 240 MET cc_start: 0.8761 (mpp) cc_final: 0.8529 (mpp) REVERT: A 354 MET cc_start: 0.8529 (mmm) cc_final: 0.8218 (mmm) REVERT: A 394 MET cc_start: 0.9112 (pmm) cc_final: 0.8707 (ppp) REVERT: A 461 ASP cc_start: 0.9122 (m-30) cc_final: 0.8845 (m-30) REVERT: A 681 TYR cc_start: 0.8205 (p90) cc_final: 0.7971 (p90) REVERT: B 158 LEU cc_start: 0.8480 (tp) cc_final: 0.8147 (tp) REVERT: B 574 VAL cc_start: 0.8482 (t) cc_final: 0.8197 (t) REVERT: B 716 ASP cc_start: 0.9044 (m-30) cc_final: 0.8804 (m-30) REVERT: C 154 MET cc_start: 0.8145 (tpt) cc_final: 0.7931 (tpt) REVERT: C 171 HIS cc_start: 0.9102 (m90) cc_final: 0.8809 (m90) REVERT: C 198 ASP cc_start: 0.8814 (t70) cc_final: 0.8562 (t0) REVERT: C 240 MET cc_start: 0.8430 (mmp) cc_final: 0.7895 (mmm) REVERT: C 317 THR cc_start: 0.8088 (p) cc_final: 0.7388 (p) REVERT: C 354 MET cc_start: 0.8227 (mmp) cc_final: 0.7647 (mmm) REVERT: C 501 MET cc_start: 0.9349 (ppp) cc_final: 0.9138 (ppp) REVERT: C 520 ASN cc_start: 0.8921 (t0) cc_final: 0.8662 (t0) REVERT: C 631 ILE cc_start: 0.9237 (mp) cc_final: 0.8755 (tp) REVERT: C 641 MET cc_start: 0.8911 (tmm) cc_final: 0.8483 (tmm) REVERT: C 642 ILE cc_start: 0.9729 (mm) cc_final: 0.9513 (mm) REVERT: C 760 ILE cc_start: 0.8911 (mm) cc_final: 0.8708 (mt) REVERT: D 142 MET cc_start: 0.8269 (ttm) cc_final: 0.7768 (ttm) REVERT: D 168 ILE cc_start: 0.8500 (pt) cc_final: 0.8059 (mt) REVERT: D 457 CYS cc_start: 0.8151 (m) cc_final: 0.7808 (m) REVERT: D 554 PHE cc_start: 0.8832 (t80) cc_final: 0.8039 (t80) REVERT: D 569 VAL cc_start: 0.9374 (t) cc_final: 0.9097 (t) REVERT: D 654 MET cc_start: 0.8928 (tpp) cc_final: 0.8373 (tmm) REVERT: D 715 ASP cc_start: 0.8957 (p0) cc_final: 0.8752 (p0) REVERT: D 743 ASP cc_start: 0.7693 (t70) cc_final: 0.7383 (t0) outliers start: 9 outliers final: 7 residues processed: 479 average time/residue: 0.2776 time to fit residues: 223.8287 Evaluate side-chains 379 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 372 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 0.6980 chunk 237 optimal weight: 0.5980 chunk 132 optimal weight: 7.9990 chunk 81 optimal weight: 30.0000 chunk 160 optimal weight: 40.0000 chunk 127 optimal weight: 5.9990 chunk 246 optimal weight: 0.0050 chunk 95 optimal weight: 0.1980 chunk 149 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 285 optimal weight: 6.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 521 ASN B 145 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 24026 Z= 0.169 Angle : 0.583 13.829 32838 Z= 0.305 Chirality : 0.043 0.437 3910 Planarity : 0.004 0.103 4184 Dihedral : 6.142 113.059 3583 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.57 % Favored : 93.27 % Rotamer: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 3136 helix: 0.34 (0.16), residues: 1109 sheet: -0.96 (0.28), residues: 367 loop : -1.72 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 197 HIS 0.004 0.001 HIS A 94 PHE 0.049 0.002 PHE B 176 TYR 0.020 0.001 TYR A 109 ARG 0.003 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 479 time to evaluate : 2.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8971 (mtp-110) cc_final: 0.8124 (ttp80) REVERT: A 155 MET cc_start: 0.8445 (tmm) cc_final: 0.8229 (tmm) REVERT: A 197 PHE cc_start: 0.7879 (t80) cc_final: 0.7487 (t80) REVERT: A 198 ASP cc_start: 0.8935 (p0) cc_final: 0.8234 (p0) REVERT: A 240 MET cc_start: 0.8730 (mpp) cc_final: 0.8418 (mpp) REVERT: A 354 MET cc_start: 0.8444 (mmm) cc_final: 0.8163 (mmm) REVERT: A 394 MET cc_start: 0.9081 (pmm) cc_final: 0.8682 (ppp) REVERT: A 461 ASP cc_start: 0.9130 (m-30) cc_final: 0.8879 (m-30) REVERT: A 470 MET cc_start: 0.9355 (mmm) cc_final: 0.8973 (mmm) REVERT: A 520 ASN cc_start: 0.9106 (t0) cc_final: 0.8694 (t0) REVERT: A 681 TYR cc_start: 0.8217 (p90) cc_final: 0.7966 (p90) REVERT: B 158 LEU cc_start: 0.8526 (tp) cc_final: 0.8185 (tp) REVERT: B 461 CYS cc_start: 0.8883 (m) cc_final: 0.8494 (m) REVERT: B 562 MET cc_start: 0.8679 (tmm) cc_final: 0.8370 (tmm) REVERT: B 716 ASP cc_start: 0.9049 (m-30) cc_final: 0.8820 (m-30) REVERT: C 171 HIS cc_start: 0.9080 (m90) cc_final: 0.8836 (m90) REVERT: C 198 ASP cc_start: 0.8816 (t70) cc_final: 0.8551 (t0) REVERT: C 317 THR cc_start: 0.7910 (p) cc_final: 0.7423 (p) REVERT: C 354 MET cc_start: 0.8341 (mmp) cc_final: 0.7848 (mmm) REVERT: C 501 MET cc_start: 0.9404 (ppp) cc_final: 0.9159 (ppp) REVERT: C 520 ASN cc_start: 0.8962 (t0) cc_final: 0.8699 (t0) REVERT: C 643 ILE cc_start: 0.9452 (mm) cc_final: 0.9248 (mm) REVERT: C 669 ASP cc_start: 0.9386 (t0) cc_final: 0.8956 (t0) REVERT: D 101 ASP cc_start: 0.8554 (t0) cc_final: 0.8189 (t70) REVERT: D 142 MET cc_start: 0.8376 (ttm) cc_final: 0.7831 (ttm) REVERT: D 457 CYS cc_start: 0.7478 (m) cc_final: 0.7165 (m) REVERT: D 524 ASP cc_start: 0.8302 (t70) cc_final: 0.7923 (t70) REVERT: D 537 MET cc_start: 0.8955 (tmm) cc_final: 0.8172 (tmm) REVERT: D 554 PHE cc_start: 0.8591 (t80) cc_final: 0.8011 (t80) REVERT: D 654 MET cc_start: 0.8843 (tpp) cc_final: 0.8398 (tmm) REVERT: D 692 GLU cc_start: 0.8903 (pt0) cc_final: 0.8692 (pt0) REVERT: D 715 ASP cc_start: 0.9026 (p0) cc_final: 0.8797 (p0) REVERT: D 732 ASP cc_start: 0.8652 (m-30) cc_final: 0.7743 (t0) REVERT: D 743 ASP cc_start: 0.7594 (t70) cc_final: 0.7266 (t0) outliers start: 1 outliers final: 1 residues processed: 480 average time/residue: 0.2736 time to fit residues: 222.0427 Evaluate side-chains 383 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 382 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 237 optimal weight: 10.0000 chunk 194 optimal weight: 0.0570 chunk 78 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 308 optimal weight: 2.9990 chunk 254 optimal weight: 10.0000 chunk 283 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 229 optimal weight: 0.7980 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 521 ASN B 145 GLN C 47 ASN C 161 ASN C 162 HIS ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN ** D 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 24026 Z= 0.184 Angle : 0.570 12.085 32838 Z= 0.295 Chirality : 0.043 0.386 3910 Planarity : 0.004 0.100 4184 Dihedral : 5.884 114.232 3583 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.66 % Favored : 93.21 % Rotamer: Outliers : 0.08 % Allowed : 3.65 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 3136 helix: 0.44 (0.16), residues: 1106 sheet: -0.81 (0.29), residues: 359 loop : -1.69 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 635 HIS 0.004 0.001 HIS A 780 PHE 0.037 0.001 PHE B 176 TYR 0.021 0.001 TYR C 526 ARG 0.002 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 478 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8967 (mtp-110) cc_final: 0.8104 (ttp80) REVERT: A 197 PHE cc_start: 0.7813 (t80) cc_final: 0.7540 (t80) REVERT: A 198 ASP cc_start: 0.8876 (p0) cc_final: 0.8270 (p0) REVERT: A 240 MET cc_start: 0.8704 (mpp) cc_final: 0.8329 (mpp) REVERT: A 317 THR cc_start: 0.7719 (p) cc_final: 0.7480 (p) REVERT: A 347 LYS cc_start: 0.8362 (tmmt) cc_final: 0.7948 (ttpp) REVERT: A 354 MET cc_start: 0.8373 (mmm) cc_final: 0.8144 (mmm) REVERT: A 394 MET cc_start: 0.9079 (pmm) cc_final: 0.8711 (ppp) REVERT: A 461 ASP cc_start: 0.9184 (m-30) cc_final: 0.8905 (m-30) REVERT: A 470 MET cc_start: 0.9337 (mmm) cc_final: 0.8901 (mmm) REVERT: A 520 ASN cc_start: 0.9138 (t0) cc_final: 0.8837 (t0) REVERT: A 528 GLU cc_start: 0.8836 (mt-10) cc_final: 0.7963 (mt-10) REVERT: A 681 TYR cc_start: 0.8290 (p90) cc_final: 0.8084 (p90) REVERT: B 158 LEU cc_start: 0.8498 (tp) cc_final: 0.8100 (tp) REVERT: B 461 CYS cc_start: 0.8980 (m) cc_final: 0.8572 (m) REVERT: B 716 ASP cc_start: 0.9064 (m-30) cc_final: 0.8840 (m-30) REVERT: C 171 HIS cc_start: 0.9095 (m90) cc_final: 0.8865 (m90) REVERT: C 198 ASP cc_start: 0.8794 (t70) cc_final: 0.8543 (t0) REVERT: C 354 MET cc_start: 0.8412 (mmp) cc_final: 0.7905 (mmm) REVERT: C 501 MET cc_start: 0.9447 (ppp) cc_final: 0.9169 (ppp) REVERT: C 520 ASN cc_start: 0.9005 (t0) cc_final: 0.8751 (t0) REVERT: C 631 ILE cc_start: 0.8859 (mp) cc_final: 0.8634 (mm) REVERT: C 669 ASP cc_start: 0.9334 (t0) cc_final: 0.8855 (t0) REVERT: D 101 ASP cc_start: 0.8603 (t0) cc_final: 0.8164 (t70) REVERT: D 142 MET cc_start: 0.8426 (ttm) cc_final: 0.7835 (ttm) REVERT: D 457 CYS cc_start: 0.7409 (m) cc_final: 0.7127 (m) REVERT: D 524 ASP cc_start: 0.8366 (t70) cc_final: 0.7938 (t0) REVERT: D 554 PHE cc_start: 0.8603 (t80) cc_final: 0.7987 (t80) REVERT: D 654 MET cc_start: 0.8799 (tpp) cc_final: 0.8467 (tpp) REVERT: D 706 MET cc_start: 0.6794 (tpt) cc_final: 0.6460 (tpt) REVERT: D 715 ASP cc_start: 0.9081 (p0) cc_final: 0.8827 (p0) REVERT: D 732 ASP cc_start: 0.8660 (m-30) cc_final: 0.7729 (t0) REVERT: D 743 ASP cc_start: 0.7627 (t70) cc_final: 0.7339 (t70) REVERT: D 793 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8732 (mm-30) outliers start: 2 outliers final: 1 residues processed: 479 average time/residue: 0.2829 time to fit residues: 229.8865 Evaluate side-chains 391 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 390 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 10.0000 chunk 214 optimal weight: 0.0270 chunk 148 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 191 optimal weight: 20.0000 chunk 286 optimal weight: 0.0060 chunk 303 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 271 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 overall best weight: 0.9656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN B 145 GLN B 615 ASN C 161 ASN C 162 HIS ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 24026 Z= 0.150 Angle : 0.568 16.333 32838 Z= 0.287 Chirality : 0.042 0.369 3910 Planarity : 0.004 0.096 4184 Dihedral : 5.634 113.368 3583 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.51 % Favored : 93.37 % Rotamer: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.15), residues: 3136 helix: 0.48 (0.16), residues: 1115 sheet: -0.73 (0.29), residues: 361 loop : -1.63 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 197 HIS 0.004 0.001 HIS A 94 PHE 0.022 0.001 PHE B 176 TYR 0.021 0.001 TYR A 109 ARG 0.003 0.000 ARG C 468 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 480 time to evaluate : 2.770 Fit side-chains revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8963 (mtp-110) cc_final: 0.8132 (ttp80) REVERT: A 197 PHE cc_start: 0.7801 (t80) cc_final: 0.7530 (t80) REVERT: A 198 ASP cc_start: 0.8825 (p0) cc_final: 0.8205 (p0) REVERT: A 240 MET cc_start: 0.8652 (mpp) cc_final: 0.8211 (mpp) REVERT: A 317 THR cc_start: 0.7760 (p) cc_final: 0.7520 (p) REVERT: A 354 MET cc_start: 0.8351 (mmm) cc_final: 0.8150 (mmp) REVERT: A 394 MET cc_start: 0.9068 (pmm) cc_final: 0.8740 (ppp) REVERT: A 461 ASP cc_start: 0.9180 (m-30) cc_final: 0.8876 (m-30) REVERT: A 470 MET cc_start: 0.9321 (mmm) cc_final: 0.8860 (mmm) REVERT: A 520 ASN cc_start: 0.9218 (t0) cc_final: 0.8860 (t0) REVERT: A 528 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8014 (mt-10) REVERT: A 565 LEU cc_start: 0.9291 (pp) cc_final: 0.9060 (tt) REVERT: B 105 GLN cc_start: 0.8383 (mp10) cc_final: 0.7942 (pm20) REVERT: B 158 LEU cc_start: 0.8540 (tp) cc_final: 0.7981 (tp) REVERT: B 285 TRP cc_start: 0.7836 (t60) cc_final: 0.7608 (t60) REVERT: B 461 CYS cc_start: 0.8956 (m) cc_final: 0.8600 (m) REVERT: B 477 ASP cc_start: 0.8822 (t0) cc_final: 0.8572 (t0) REVERT: B 562 MET cc_start: 0.8959 (tmm) cc_final: 0.8660 (tmm) REVERT: B 716 ASP cc_start: 0.9068 (m-30) cc_final: 0.8841 (m-30) REVERT: C 198 ASP cc_start: 0.8798 (t70) cc_final: 0.8545 (t0) REVERT: C 240 MET cc_start: 0.8077 (mmp) cc_final: 0.7292 (mmm) REVERT: C 317 THR cc_start: 0.7823 (p) cc_final: 0.7346 (p) REVERT: C 354 MET cc_start: 0.8496 (mmp) cc_final: 0.7946 (mmm) REVERT: C 520 ASN cc_start: 0.9006 (t0) cc_final: 0.8765 (t0) REVERT: C 641 MET cc_start: 0.9032 (tmm) cc_final: 0.8591 (tmm) REVERT: C 642 ILE cc_start: 0.9637 (mm) cc_final: 0.9398 (mm) REVERT: C 643 ILE cc_start: 0.9462 (mm) cc_final: 0.9227 (mm) REVERT: C 669 ASP cc_start: 0.9290 (t0) cc_final: 0.8854 (t0) REVERT: D 101 ASP cc_start: 0.8551 (t0) cc_final: 0.8188 (t70) REVERT: D 457 CYS cc_start: 0.7447 (m) cc_final: 0.7169 (m) REVERT: D 524 ASP cc_start: 0.8389 (t70) cc_final: 0.7927 (t0) REVERT: D 554 PHE cc_start: 0.8492 (t80) cc_final: 0.7887 (t80) REVERT: D 654 MET cc_start: 0.8738 (tpp) cc_final: 0.8515 (tpp) REVERT: D 692 GLU cc_start: 0.8815 (pt0) cc_final: 0.8600 (pt0) REVERT: D 715 ASP cc_start: 0.9103 (p0) cc_final: 0.8836 (p0) REVERT: D 732 ASP cc_start: 0.8725 (m-30) cc_final: 0.7733 (t0) REVERT: D 743 ASP cc_start: 0.7551 (t70) cc_final: 0.7258 (t70) outliers start: 1 outliers final: 0 residues processed: 480 average time/residue: 0.2836 time to fit residues: 230.5409 Evaluate side-chains 391 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 225 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 259 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 154 optimal weight: 3.9990 chunk 272 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN A 162 HIS A 276 ASN A 358 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN C 161 ASN C 162 HIS C 293 HIS ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 24026 Z= 0.427 Angle : 0.745 15.793 32838 Z= 0.388 Chirality : 0.046 0.520 3910 Planarity : 0.005 0.092 4184 Dihedral : 6.288 112.324 3583 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.98 % Favored : 89.89 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 3136 helix: 0.16 (0.15), residues: 1097 sheet: -1.08 (0.28), residues: 351 loop : -1.89 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 635 HIS 0.011 0.002 HIS A 780 PHE 0.032 0.003 PHE B 176 TYR 0.023 0.002 TYR A 681 ARG 0.006 0.001 ARG D 292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 3.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.9013 (mtp-110) cc_final: 0.8092 (ttp80) REVERT: A 197 PHE cc_start: 0.7838 (t80) cc_final: 0.7539 (t80) REVERT: A 198 ASP cc_start: 0.8913 (p0) cc_final: 0.8288 (p0) REVERT: A 240 MET cc_start: 0.8789 (mpp) cc_final: 0.8527 (mpp) REVERT: A 394 MET cc_start: 0.9096 (pmm) cc_final: 0.8778 (ppp) REVERT: A 461 ASP cc_start: 0.9152 (m-30) cc_final: 0.8880 (m-30) REVERT: A 470 MET cc_start: 0.9356 (mmm) cc_final: 0.8901 (mmm) REVERT: A 497 GLU cc_start: 0.8679 (pm20) cc_final: 0.8414 (pm20) REVERT: A 811 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8321 (tm-30) REVERT: B 105 GLN cc_start: 0.8435 (mp10) cc_final: 0.8081 (pm20) REVERT: B 289 LEU cc_start: 0.8383 (mm) cc_final: 0.8123 (mm) REVERT: B 562 MET cc_start: 0.8914 (tmm) cc_final: 0.8623 (tmm) REVERT: B 716 ASP cc_start: 0.9197 (m-30) cc_final: 0.8981 (m-30) REVERT: C 42 PHE cc_start: 0.9404 (t80) cc_final: 0.9086 (t80) REVERT: C 154 MET cc_start: 0.8311 (tpt) cc_final: 0.8004 (tpt) REVERT: C 171 HIS cc_start: 0.9146 (m90) cc_final: 0.8850 (m90) REVERT: C 354 MET cc_start: 0.8370 (mmp) cc_final: 0.7885 (mmm) REVERT: C 520 ASN cc_start: 0.9003 (t0) cc_final: 0.8737 (t0) REVERT: C 641 MET cc_start: 0.9197 (tmm) cc_final: 0.8692 (tmm) REVERT: C 642 ILE cc_start: 0.9668 (mm) cc_final: 0.9391 (mm) REVERT: C 669 ASP cc_start: 0.9483 (t0) cc_final: 0.9073 (t0) REVERT: C 762 MET cc_start: 0.8822 (mtp) cc_final: 0.8397 (mtm) REVERT: D 99 PHE cc_start: 0.8867 (t80) cc_final: 0.8562 (t80) REVERT: D 101 ASP cc_start: 0.8813 (t0) cc_final: 0.8539 (t0) REVERT: D 142 MET cc_start: 0.8645 (mmt) cc_final: 0.7574 (ttm) REVERT: D 192 ASN cc_start: 0.9310 (t0) cc_final: 0.9078 (t0) REVERT: D 358 MET cc_start: 0.8485 (mmt) cc_final: 0.8144 (mmp) REVERT: D 457 CYS cc_start: 0.7533 (m) cc_final: 0.7267 (m) REVERT: D 461 CYS cc_start: 0.9298 (m) cc_final: 0.9045 (m) REVERT: D 554 PHE cc_start: 0.8594 (t80) cc_final: 0.7945 (t80) REVERT: D 692 GLU cc_start: 0.8825 (pt0) cc_final: 0.8517 (pt0) REVERT: D 715 ASP cc_start: 0.9056 (p0) cc_final: 0.8827 (p0) REVERT: D 743 ASP cc_start: 0.7685 (t70) cc_final: 0.7301 (t70) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.2714 time to fit residues: 198.9482 Evaluate side-chains 349 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 10.0000 chunk 273 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 303 optimal weight: 1.9990 chunk 252 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 159 optimal weight: 30.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS A 276 ASN A 521 ASN B 145 GLN C 161 ASN C 162 HIS ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 ASN D 817 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 24026 Z= 0.195 Angle : 0.603 15.359 32838 Z= 0.308 Chirality : 0.044 0.437 3910 Planarity : 0.004 0.090 4184 Dihedral : 5.955 113.724 3583 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.82 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.15), residues: 3136 helix: 0.47 (0.16), residues: 1098 sheet: -0.99 (0.28), residues: 349 loop : -1.78 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 197 HIS 0.004 0.001 HIS A 94 PHE 0.039 0.002 PHE B 176 TYR 0.022 0.001 TYR A 526 ARG 0.005 0.000 ARG C 704 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.9010 (mtp-110) cc_final: 0.8098 (ttp80) REVERT: A 197 PHE cc_start: 0.7791 (t80) cc_final: 0.7523 (t80) REVERT: A 198 ASP cc_start: 0.8802 (p0) cc_final: 0.8493 (t0) REVERT: A 354 MET cc_start: 0.8230 (mmp) cc_final: 0.7802 (mmm) REVERT: A 394 MET cc_start: 0.9045 (pmm) cc_final: 0.8757 (ppp) REVERT: A 461 ASP cc_start: 0.9093 (m-30) cc_final: 0.8849 (m-30) REVERT: A 470 MET cc_start: 0.9293 (mmm) cc_final: 0.8827 (mmm) REVERT: A 528 GLU cc_start: 0.8681 (mt-10) cc_final: 0.7871 (mt-10) REVERT: A 565 LEU cc_start: 0.9297 (pp) cc_final: 0.9036 (tt) REVERT: A 641 MET cc_start: 0.8768 (tmm) cc_final: 0.8516 (tmm) REVERT: A 706 MET cc_start: 0.9189 (ttp) cc_final: 0.7908 (tmm) REVERT: A 710 ASN cc_start: 0.9156 (m-40) cc_final: 0.8737 (m-40) REVERT: A 811 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8266 (tm-30) REVERT: B 105 GLN cc_start: 0.8428 (mp10) cc_final: 0.8034 (pm20) REVERT: B 158 LEU cc_start: 0.8582 (tp) cc_final: 0.8124 (tp) REVERT: B 192 ASN cc_start: 0.9056 (t0) cc_final: 0.8674 (m110) REVERT: B 477 ASP cc_start: 0.8858 (t70) cc_final: 0.8593 (t0) REVERT: B 716 ASP cc_start: 0.9165 (m-30) cc_final: 0.8955 (m-30) REVERT: C 154 MET cc_start: 0.8277 (tpt) cc_final: 0.7972 (tpt) REVERT: C 171 HIS cc_start: 0.9143 (m90) cc_final: 0.8922 (m90) REVERT: C 240 MET cc_start: 0.8130 (mmp) cc_final: 0.7361 (mmm) REVERT: C 354 MET cc_start: 0.8417 (mmp) cc_final: 0.7836 (mmm) REVERT: C 520 ASN cc_start: 0.9014 (t0) cc_final: 0.8769 (t0) REVERT: C 528 GLU cc_start: 0.8202 (mp0) cc_final: 0.7859 (mp0) REVERT: C 639 PHE cc_start: 0.9450 (t80) cc_final: 0.9195 (t80) REVERT: C 641 MET cc_start: 0.9130 (tmm) cc_final: 0.8592 (tmm) REVERT: C 642 ILE cc_start: 0.9663 (mm) cc_final: 0.9367 (mm) REVERT: C 762 MET cc_start: 0.8568 (mtp) cc_final: 0.8190 (mtm) REVERT: D 358 MET cc_start: 0.8484 (mmt) cc_final: 0.8025 (mmp) REVERT: D 457 CYS cc_start: 0.7415 (m) cc_final: 0.7144 (m) REVERT: D 524 ASP cc_start: 0.8448 (t70) cc_final: 0.8025 (t0) REVERT: D 537 MET cc_start: 0.8855 (tmm) cc_final: 0.8217 (tmm) REVERT: D 554 PHE cc_start: 0.8498 (t80) cc_final: 0.7859 (t80) REVERT: D 654 MET cc_start: 0.9048 (tpp) cc_final: 0.8501 (tpp) REVERT: D 715 ASP cc_start: 0.9109 (p0) cc_final: 0.8878 (p0) REVERT: D 732 ASP cc_start: 0.8614 (m-30) cc_final: 0.7794 (t0) REVERT: D 743 ASP cc_start: 0.7496 (t70) cc_final: 0.7118 (t70) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.2726 time to fit residues: 210.6241 Evaluate side-chains 374 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 8.9990 chunk 34 optimal weight: 30.0000 chunk 173 optimal weight: 0.6980 chunk 221 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 255 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 chunk 302 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 521 ASN B 145 GLN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 ASN D 192 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24026 Z= 0.192 Angle : 0.598 17.153 32838 Z= 0.303 Chirality : 0.043 0.415 3910 Planarity : 0.004 0.088 4184 Dihedral : 5.806 113.345 3583 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.78 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.15), residues: 3136 helix: 0.50 (0.16), residues: 1098 sheet: -0.96 (0.29), residues: 347 loop : -1.73 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 635 HIS 0.005 0.001 HIS A 38 PHE 0.026 0.001 PHE B 176 TYR 0.018 0.001 TYR A 526 ARG 0.004 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9421 (ppp) cc_final: 0.9168 (ppp) REVERT: A 115 ARG cc_start: 0.9029 (mtp-110) cc_final: 0.8141 (ttp80) REVERT: A 197 PHE cc_start: 0.7800 (t80) cc_final: 0.7520 (t80) REVERT: A 198 ASP cc_start: 0.8797 (p0) cc_final: 0.8474 (t0) REVERT: A 240 MET cc_start: 0.8639 (mpp) cc_final: 0.8350 (mpp) REVERT: A 354 MET cc_start: 0.8256 (mmp) cc_final: 0.7826 (mmm) REVERT: A 394 MET cc_start: 0.9014 (pmm) cc_final: 0.8784 (ppp) REVERT: A 461 ASP cc_start: 0.9120 (m-30) cc_final: 0.8870 (m-30) REVERT: A 470 MET cc_start: 0.9316 (mmm) cc_final: 0.8840 (mmm) REVERT: A 520 ASN cc_start: 0.9219 (t0) cc_final: 0.8843 (t0) REVERT: A 528 GLU cc_start: 0.8699 (mt-10) cc_final: 0.7831 (mt-10) REVERT: A 706 MET cc_start: 0.9149 (ttp) cc_final: 0.7911 (tmm) REVERT: A 710 ASN cc_start: 0.9200 (m-40) cc_final: 0.8736 (m-40) REVERT: A 811 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8215 (tm-30) REVERT: B 105 GLN cc_start: 0.8438 (mp10) cc_final: 0.8069 (pm20) REVERT: B 158 LEU cc_start: 0.8469 (tp) cc_final: 0.8102 (tp) REVERT: B 192 ASN cc_start: 0.8989 (t0) cc_final: 0.8630 (m110) REVERT: B 477 ASP cc_start: 0.8830 (t70) cc_final: 0.8553 (t0) REVERT: B 716 ASP cc_start: 0.9188 (m-30) cc_final: 0.8972 (m-30) REVERT: C 154 MET cc_start: 0.8246 (tpt) cc_final: 0.7981 (tpt) REVERT: C 171 HIS cc_start: 0.9139 (m90) cc_final: 0.8934 (m90) REVERT: C 198 ASP cc_start: 0.8547 (t70) cc_final: 0.8302 (t0) REVERT: C 354 MET cc_start: 0.8457 (mmp) cc_final: 0.7880 (mmm) REVERT: C 520 ASN cc_start: 0.8993 (t0) cc_final: 0.8738 (t0) REVERT: C 528 GLU cc_start: 0.8121 (mp0) cc_final: 0.7866 (mp0) REVERT: C 639 PHE cc_start: 0.9449 (t80) cc_final: 0.9217 (t80) REVERT: C 641 MET cc_start: 0.9107 (tmm) cc_final: 0.8581 (tmm) REVERT: C 642 ILE cc_start: 0.9666 (mm) cc_final: 0.9392 (mm) REVERT: C 762 MET cc_start: 0.8570 (mtp) cc_final: 0.8220 (mtm) REVERT: D 101 ASP cc_start: 0.8776 (t0) cc_final: 0.8490 (t0) REVERT: D 142 MET cc_start: 0.8548 (tpp) cc_final: 0.8001 (ttm) REVERT: D 358 MET cc_start: 0.8514 (mmt) cc_final: 0.8154 (mmp) REVERT: D 457 CYS cc_start: 0.7500 (m) cc_final: 0.7249 (m) REVERT: D 524 ASP cc_start: 0.8462 (t70) cc_final: 0.8061 (t0) REVERT: D 537 MET cc_start: 0.8854 (tmm) cc_final: 0.8239 (tmm) REVERT: D 554 PHE cc_start: 0.8473 (t80) cc_final: 0.7836 (t80) REVERT: D 654 MET cc_start: 0.8975 (tpp) cc_final: 0.8465 (tpp) REVERT: D 692 GLU cc_start: 0.8887 (pt0) cc_final: 0.8598 (pt0) REVERT: D 715 ASP cc_start: 0.9119 (p0) cc_final: 0.8884 (p0) REVERT: D 732 ASP cc_start: 0.8577 (m-30) cc_final: 0.7910 (t70) REVERT: D 743 ASP cc_start: 0.7434 (t70) cc_final: 0.7062 (t70) REVERT: D 793 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8695 (mm-30) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.2737 time to fit residues: 216.8980 Evaluate side-chains 370 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 237 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 521 ASN B 145 GLN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 ASN ** D 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 24026 Z= 0.162 Angle : 0.592 18.079 32838 Z= 0.298 Chirality : 0.043 0.376 3910 Planarity : 0.004 0.086 4184 Dihedral : 5.655 113.267 3583 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.70 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 3136 helix: 0.54 (0.16), residues: 1099 sheet: -0.83 (0.28), residues: 357 loop : -1.67 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 635 HIS 0.003 0.001 HIS A 38 PHE 0.023 0.001 PHE D 637 TYR 0.030 0.001 TYR D 389 ARG 0.003 0.000 ARG C 704 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 470 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9438 (ppp) cc_final: 0.9193 (ppp) REVERT: A 115 ARG cc_start: 0.9027 (mtp-110) cc_final: 0.8158 (ttp80) REVERT: A 155 MET cc_start: 0.8468 (tmm) cc_final: 0.8254 (tmm) REVERT: A 197 PHE cc_start: 0.7766 (t80) cc_final: 0.7491 (t80) REVERT: A 198 ASP cc_start: 0.8768 (p0) cc_final: 0.8466 (t0) REVERT: A 240 MET cc_start: 0.8543 (mpp) cc_final: 0.8232 (mpp) REVERT: A 354 MET cc_start: 0.8267 (mmp) cc_final: 0.7800 (mmm) REVERT: A 394 MET cc_start: 0.9022 (pmm) cc_final: 0.8781 (ppp) REVERT: A 461 ASP cc_start: 0.9111 (m-30) cc_final: 0.8859 (m-30) REVERT: A 470 MET cc_start: 0.9279 (mmm) cc_final: 0.8808 (mmm) REVERT: A 520 ASN cc_start: 0.9205 (t0) cc_final: 0.8803 (t0) REVERT: A 528 GLU cc_start: 0.8514 (mt-10) cc_final: 0.7747 (mt-10) REVERT: A 799 ASP cc_start: 0.8544 (p0) cc_final: 0.8324 (p0) REVERT: A 811 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8397 (tm-30) REVERT: B 105 GLN cc_start: 0.8441 (mp10) cc_final: 0.8055 (pm20) REVERT: B 150 ILE cc_start: 0.8678 (pt) cc_final: 0.8453 (pt) REVERT: B 158 LEU cc_start: 0.8444 (tp) cc_final: 0.8085 (tp) REVERT: B 192 ASN cc_start: 0.8949 (t0) cc_final: 0.8626 (m110) REVERT: B 477 ASP cc_start: 0.8763 (t70) cc_final: 0.8469 (t0) REVERT: B 498 ILE cc_start: 0.8550 (mm) cc_final: 0.8301 (mm) REVERT: B 559 TRP cc_start: 0.6561 (m-10) cc_final: 0.6167 (m-10) REVERT: B 716 ASP cc_start: 0.9187 (m-30) cc_final: 0.8981 (m-30) REVERT: B 812 GLN cc_start: 0.8059 (tp-100) cc_final: 0.7847 (tp-100) REVERT: C 109 TYR cc_start: 0.8050 (p90) cc_final: 0.7784 (p90) REVERT: C 154 MET cc_start: 0.8218 (tpt) cc_final: 0.7917 (tpt) REVERT: C 198 ASP cc_start: 0.8566 (t70) cc_final: 0.8332 (t0) REVERT: C 354 MET cc_start: 0.8525 (mmp) cc_final: 0.7943 (mmm) REVERT: C 520 ASN cc_start: 0.8972 (t0) cc_final: 0.8716 (t0) REVERT: C 528 GLU cc_start: 0.8194 (mp0) cc_final: 0.7894 (mp0) REVERT: C 540 ILE cc_start: 0.9133 (mm) cc_final: 0.8860 (mm) REVERT: C 639 PHE cc_start: 0.9423 (t80) cc_final: 0.9206 (t80) REVERT: C 641 MET cc_start: 0.9088 (tmm) cc_final: 0.8556 (tmm) REVERT: C 642 ILE cc_start: 0.9661 (mm) cc_final: 0.9392 (mm) REVERT: C 710 ASN cc_start: 0.9108 (p0) cc_final: 0.8886 (p0) REVERT: C 762 MET cc_start: 0.8472 (mtp) cc_final: 0.8242 (mtm) REVERT: C 795 TYR cc_start: 0.8169 (p90) cc_final: 0.7789 (p90) REVERT: D 101 ASP cc_start: 0.8764 (t0) cc_final: 0.8487 (t0) REVERT: D 142 MET cc_start: 0.8580 (tpp) cc_final: 0.8062 (ttm) REVERT: D 457 CYS cc_start: 0.7471 (m) cc_final: 0.7252 (m) REVERT: D 508 MET cc_start: 0.9065 (tpt) cc_final: 0.8851 (tpt) REVERT: D 524 ASP cc_start: 0.8454 (t70) cc_final: 0.8209 (t0) REVERT: D 537 MET cc_start: 0.8826 (tmm) cc_final: 0.8265 (tmm) REVERT: D 554 PHE cc_start: 0.8447 (t80) cc_final: 0.7819 (t80) REVERT: D 654 MET cc_start: 0.8877 (tpp) cc_final: 0.8416 (tpp) REVERT: D 692 GLU cc_start: 0.8865 (pt0) cc_final: 0.8552 (pt0) REVERT: D 715 ASP cc_start: 0.9134 (p0) cc_final: 0.8897 (p0) REVERT: D 732 ASP cc_start: 0.8557 (m-30) cc_final: 0.7914 (t70) REVERT: D 743 ASP cc_start: 0.7252 (t70) cc_final: 0.6897 (t70) outliers start: 0 outliers final: 0 residues processed: 470 average time/residue: 0.2709 time to fit residues: 217.2926 Evaluate side-chains 389 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 6.9990 chunk 289 optimal weight: 0.9980 chunk 264 optimal weight: 0.0070 chunk 282 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 266 optimal weight: 9.9990 chunk 281 optimal weight: 0.9980 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 521 ASN B 145 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 ASN D 184 ASN ** D 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 24026 Z= 0.157 Angle : 0.600 19.070 32838 Z= 0.298 Chirality : 0.043 0.362 3910 Planarity : 0.004 0.083 4184 Dihedral : 5.487 113.356 3583 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.66 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 3136 helix: 0.58 (0.16), residues: 1103 sheet: -0.66 (0.29), residues: 363 loop : -1.62 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 285 HIS 0.003 0.000 HIS A 38 PHE 0.022 0.001 PHE A 639 TYR 0.023 0.001 TYR D 389 ARG 0.003 0.000 ARG C 704 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 470 time to evaluate : 2.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9433 (ppp) cc_final: 0.9175 (ppp) REVERT: A 115 ARG cc_start: 0.9036 (mtp-110) cc_final: 0.8125 (ttp80) REVERT: A 155 MET cc_start: 0.8440 (tmm) cc_final: 0.8231 (tmm) REVERT: A 197 PHE cc_start: 0.7751 (t80) cc_final: 0.7480 (t80) REVERT: A 198 ASP cc_start: 0.8723 (p0) cc_final: 0.8438 (t0) REVERT: A 240 MET cc_start: 0.8517 (mpp) cc_final: 0.8192 (mpp) REVERT: A 354 MET cc_start: 0.8245 (mmp) cc_final: 0.7801 (mmm) REVERT: A 394 MET cc_start: 0.8995 (pmm) cc_final: 0.8771 (ppp) REVERT: A 461 ASP cc_start: 0.9115 (m-30) cc_final: 0.8884 (m-30) REVERT: A 470 MET cc_start: 0.9287 (mmm) cc_final: 0.8829 (mmm) REVERT: A 520 ASN cc_start: 0.9169 (t0) cc_final: 0.8776 (t0) REVERT: A 528 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7694 (mt-10) REVERT: A 581 ASP cc_start: 0.6380 (p0) cc_final: 0.6172 (p0) REVERT: A 616 ASN cc_start: 0.9284 (t0) cc_final: 0.9054 (t0) REVERT: A 811 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8393 (tm-30) REVERT: B 105 GLN cc_start: 0.8445 (mp10) cc_final: 0.8064 (pm20) REVERT: B 158 LEU cc_start: 0.8433 (tp) cc_final: 0.8065 (tp) REVERT: B 192 ASN cc_start: 0.8899 (t0) cc_final: 0.8613 (m110) REVERT: B 306 ASP cc_start: 0.8394 (t0) cc_final: 0.7863 (m-30) REVERT: B 477 ASP cc_start: 0.8703 (t70) cc_final: 0.8403 (t0) REVERT: B 716 ASP cc_start: 0.9172 (m-30) cc_final: 0.8965 (m-30) REVERT: B 812 GLN cc_start: 0.8025 (tp-100) cc_final: 0.7823 (tp-100) REVERT: C 109 TYR cc_start: 0.8022 (p90) cc_final: 0.7754 (p90) REVERT: C 154 MET cc_start: 0.8134 (tpt) cc_final: 0.7841 (tpt) REVERT: C 171 HIS cc_start: 0.9060 (m90) cc_final: 0.8849 (m90) REVERT: C 198 ASP cc_start: 0.8576 (t70) cc_final: 0.8340 (t0) REVERT: C 354 MET cc_start: 0.8549 (mmp) cc_final: 0.8025 (mmm) REVERT: C 520 ASN cc_start: 0.8968 (t0) cc_final: 0.8731 (t0) REVERT: C 528 GLU cc_start: 0.8150 (mp0) cc_final: 0.7880 (mp0) REVERT: C 536 GLN cc_start: 0.8153 (pp30) cc_final: 0.7722 (pp30) REVERT: C 540 ILE cc_start: 0.9114 (mm) cc_final: 0.8862 (mm) REVERT: C 639 PHE cc_start: 0.9380 (t80) cc_final: 0.9179 (t80) REVERT: C 641 MET cc_start: 0.9076 (tmm) cc_final: 0.8552 (tmm) REVERT: C 642 ILE cc_start: 0.9655 (mm) cc_final: 0.9396 (mm) REVERT: C 762 MET cc_start: 0.8395 (mtp) cc_final: 0.8188 (mtm) REVERT: C 795 TYR cc_start: 0.8136 (p90) cc_final: 0.7807 (p90) REVERT: D 101 ASP cc_start: 0.8702 (t0) cc_final: 0.8415 (t0) REVERT: D 142 MET cc_start: 0.8606 (tpp) cc_final: 0.8092 (ttm) REVERT: D 161 MET cc_start: 0.8874 (mmp) cc_final: 0.8378 (mtm) REVERT: D 457 CYS cc_start: 0.7513 (m) cc_final: 0.7301 (m) REVERT: D 524 ASP cc_start: 0.8452 (t70) cc_final: 0.8194 (t0) REVERT: D 554 PHE cc_start: 0.8435 (t80) cc_final: 0.7776 (t80) REVERT: D 654 MET cc_start: 0.8784 (tpp) cc_final: 0.8435 (tpp) REVERT: D 692 GLU cc_start: 0.8862 (pt0) cc_final: 0.8549 (pt0) REVERT: D 706 MET cc_start: 0.6699 (tpt) cc_final: 0.6402 (tpt) REVERT: D 715 ASP cc_start: 0.9135 (p0) cc_final: 0.8889 (p0) REVERT: D 732 ASP cc_start: 0.8607 (m-30) cc_final: 0.7982 (t70) REVERT: D 743 ASP cc_start: 0.6984 (t70) cc_final: 0.6673 (t70) outliers start: 0 outliers final: 0 residues processed: 470 average time/residue: 0.2842 time to fit residues: 227.6651 Evaluate side-chains 388 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 30.0000 chunk 298 optimal weight: 0.1980 chunk 182 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 207 optimal weight: 0.6980 chunk 312 optimal weight: 0.8980 chunk 287 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 521 ASN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN B 649 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 24026 Z= 0.161 Angle : 0.593 19.850 32838 Z= 0.295 Chirality : 0.043 0.360 3910 Planarity : 0.004 0.080 4184 Dihedral : 5.382 113.197 3583 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.44 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.15), residues: 3136 helix: 0.55 (0.16), residues: 1115 sheet: -0.60 (0.29), residues: 355 loop : -1.61 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 285 HIS 0.003 0.001 HIS A 38 PHE 0.025 0.001 PHE A 639 TYR 0.020 0.001 TYR C 526 ARG 0.003 0.000 ARG C 704 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 471 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9427 (ppp) cc_final: 0.9214 (ppp) REVERT: A 115 ARG cc_start: 0.9041 (mtp-110) cc_final: 0.8159 (ttp80) REVERT: A 155 MET cc_start: 0.8488 (tmm) cc_final: 0.8275 (tmm) REVERT: A 197 PHE cc_start: 0.7720 (t80) cc_final: 0.7444 (t80) REVERT: A 198 ASP cc_start: 0.8696 (p0) cc_final: 0.8421 (t0) REVERT: A 240 MET cc_start: 0.8497 (mpp) cc_final: 0.8172 (mpp) REVERT: A 354 MET cc_start: 0.8288 (mmp) cc_final: 0.7830 (mmm) REVERT: A 394 MET cc_start: 0.8997 (pmm) cc_final: 0.8760 (ppp) REVERT: A 461 ASP cc_start: 0.9116 (m-30) cc_final: 0.8798 (t70) REVERT: A 470 MET cc_start: 0.9264 (mmm) cc_final: 0.8794 (mmm) REVERT: A 497 GLU cc_start: 0.8574 (pm20) cc_final: 0.8257 (pm20) REVERT: A 520 ASN cc_start: 0.9114 (t0) cc_final: 0.8803 (t0) REVERT: A 528 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7648 (mt-10) REVERT: A 616 ASN cc_start: 0.9294 (t0) cc_final: 0.9085 (t0) REVERT: A 811 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8390 (tm-30) REVERT: B 105 GLN cc_start: 0.8394 (mp10) cc_final: 0.8030 (pm20) REVERT: B 158 LEU cc_start: 0.8422 (tp) cc_final: 0.8032 (tp) REVERT: B 192 ASN cc_start: 0.8852 (t0) cc_final: 0.8577 (m110) REVERT: B 285 TRP cc_start: 0.7870 (t60) cc_final: 0.7667 (t60) REVERT: B 306 ASP cc_start: 0.8428 (t0) cc_final: 0.7897 (m-30) REVERT: B 477 ASP cc_start: 0.8706 (t70) cc_final: 0.8406 (t0) REVERT: B 649 ASN cc_start: 0.8537 (t0) cc_final: 0.8134 (t0) REVERT: B 716 ASP cc_start: 0.9172 (m-30) cc_final: 0.8956 (m-30) REVERT: C 109 TYR cc_start: 0.7969 (p90) cc_final: 0.7726 (p90) REVERT: C 154 MET cc_start: 0.8110 (tpt) cc_final: 0.7846 (tpt) REVERT: C 171 HIS cc_start: 0.9063 (m90) cc_final: 0.8862 (m90) REVERT: C 198 ASP cc_start: 0.8595 (t70) cc_final: 0.8365 (t0) REVERT: C 240 MET cc_start: 0.7778 (mmm) cc_final: 0.6822 (mmm) REVERT: C 354 MET cc_start: 0.8553 (mmp) cc_final: 0.8036 (mmm) REVERT: C 520 ASN cc_start: 0.8953 (t0) cc_final: 0.8708 (t0) REVERT: C 528 GLU cc_start: 0.8141 (mp0) cc_final: 0.7843 (mp0) REVERT: C 540 ILE cc_start: 0.9113 (mm) cc_final: 0.8869 (mm) REVERT: C 641 MET cc_start: 0.9065 (tmm) cc_final: 0.8550 (tmm) REVERT: C 642 ILE cc_start: 0.9656 (mm) cc_final: 0.9402 (mm) REVERT: C 762 MET cc_start: 0.8388 (mtp) cc_final: 0.8172 (mtm) REVERT: C 795 TYR cc_start: 0.8133 (p90) cc_final: 0.7798 (p90) REVERT: D 101 ASP cc_start: 0.8697 (t0) cc_final: 0.8402 (t0) REVERT: D 142 MET cc_start: 0.8584 (tpp) cc_final: 0.8136 (ttm) REVERT: D 457 CYS cc_start: 0.7517 (m) cc_final: 0.7303 (m) REVERT: D 524 ASP cc_start: 0.8460 (t70) cc_final: 0.8203 (t0) REVERT: D 554 PHE cc_start: 0.8440 (t80) cc_final: 0.7788 (t80) REVERT: D 565 MET cc_start: 0.9369 (tpt) cc_final: 0.9093 (tpt) REVERT: D 654 MET cc_start: 0.8773 (tpp) cc_final: 0.8384 (tpp) REVERT: D 692 GLU cc_start: 0.8862 (pt0) cc_final: 0.8539 (pt0) REVERT: D 706 MET cc_start: 0.6592 (tpt) cc_final: 0.6240 (tpt) REVERT: D 715 ASP cc_start: 0.9128 (p0) cc_final: 0.8878 (p0) REVERT: D 732 ASP cc_start: 0.8585 (m-30) cc_final: 0.7966 (t70) REVERT: D 743 ASP cc_start: 0.7002 (t70) cc_final: 0.6733 (t0) outliers start: 0 outliers final: 0 residues processed: 471 average time/residue: 0.2668 time to fit residues: 213.0130 Evaluate side-chains 399 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 2.9990 chunk 265 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 249 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 256 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN C 270 GLN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.125175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.092178 restraints weight = 64776.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.095184 restraints weight = 38401.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097218 restraints weight = 27050.414| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 24026 Z= 0.151 Angle : 0.593 20.174 32838 Z= 0.291 Chirality : 0.043 0.357 3910 Planarity : 0.004 0.078 4184 Dihedral : 5.261 112.941 3583 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.54 % Favored : 93.34 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 3136 helix: 0.55 (0.16), residues: 1116 sheet: -0.59 (0.29), residues: 352 loop : -1.54 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 285 HIS 0.003 0.000 HIS A 38 PHE 0.020 0.001 PHE D 653 TYR 0.020 0.001 TYR C 526 ARG 0.002 0.000 ARG C 695 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5026.22 seconds wall clock time: 91 minutes 40.02 seconds (5500.02 seconds total)